Analysis workflow for detection of genome-wide variations in TASUKE+ of RAP-DB
Genome-wide variation data among >500 accessions was provided in the multiple genome browser TASUKE+ of RAP-DB. Here we provide the analysis workflow for detection of the genome-wide variations (SNPs/InDels). |
Reference data
- Genome sequences [FASTA]
- IRGSP-1.0 genome (including organella and unanchored contig sequences)
- Gene annotation for snpEff [Annotation GTF] [Protein FASTA]
- RAP-DB (both representative and predicted genes as of 26 Nov 2018)
- MSU (all genes in RGAP 7)
- Illumina adapter sequences attached to the Trimmomatic program (TruSeq2 PE + TruSeq3 PE)
- Chromosome information (chromosome_list.csv) for TASUKE+
$ cat chromosome_list.csv chr01,43270923,16610866,17243770 chr02,35937250,13541821,13872411 chr03,36413819,19431743,19745569 chr04,35502694,9744480,9973218 chr05,29958434,12390387,12627019 chr06,31248787,15332004,15555636 chr07,29697621,11887856,12272916 chr08,28443022,12847483,13061068 chr09,23012720,2749793,3043847 chr10,23207287,8082722,8309866 chr11,29021106,12039480,12482616 chr12,27531856,11761737,12103486
Analysis tools
- Java (JDK 1.8.0_191)
- FastQC v0.11.8
- BWA (bwa v0.7.17)
- SamTools (v1.9)
- BamTools (as of 4 Dec 2018)
- GATK (v4.0.11.0)
- Trimmomatic (v0.38)
- Picard (v2.18.17)
- SnpEff (v4.3t)
- TASUKE+ (version 20190826)
Commands and parameters used in the workflow
- Preprocessing of Illumina paired-end reads
- Making index of the genome
- Alignment of Illumina reads to the reference genome
- Make clean BAM
- Remove PCR duplicates
- Variant detection and filtering by GATK
- Run SnpEff
- Make depth data for TASUKE+
- Upload variation and depth data to TASUKE+
$ java -jar trimmomatic-0.38.jar PE \ -phred33 read.r1.fastq.gz read.r2.fastq.gz \ read.pe.r1.fastq.gz read.se.r1.fastq.gz read.pe.r2.fastq.gz read.se.r2.fastq.gz \ ILLUMINACLIP:adapters.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:10:20 MINLEN:30
$ bwa index genome.fa $ samtools faidx genome.fa $ java -jar picard.jar CreateSequenceDictionary \ REFERENCE=genome.fa \ OUTPUT=genome.dict
$ bwa mem -M genome.fa read.pe.r1.fastq.gz read.pe.r2.fastq.gz \ | samtools sort -o alignment.sort.bam - $ samtools index alignment.sort.bam
$ java -jar picard.jar FastqToSam \ FASTQ=read.pe.r1.fastq.gz \ FASTQ2=read.pe.r2.fastq.gz \ OUTPUT=uBAM.bam \ READ_GROUP_NAME=${SAMPLE_ID} \ SAMPLE_NAME=${SAMPLE_ID} \ LIBRARY_NAME=${SAMPLE_ID} \ $ java -jar picard.jar MergeBamAlignment \ ALIGNED=alignment.sort.bam \ UNMAPPED=uBAM.bam \ OUTPUT=alignment.merge.bam \ REFERENCE_SEQUENCE=genome.fa
*User can specify any sample ID in the variable “${SAMPLE_ID}”.
$ java -jar picard.jar MarkDuplicates \ INPUT=alignment.merge.bam \ OUTPUT=alignment.rmdup.bam \ METRICS_FILE=rmdup.matrix \ REMOVE_DUPLICATES=true \ MAX_RECORDS_IN_RAM=1000000 \ TMP_DIR=./tmp $ samtools index alignment.rmdup.bam
$ gatk HaplotypeCaller \ --input alignment.rmdup.bam \ --output variants.g.vcf.gz \ --reference genome.fa \ -max-alternate-alleles 2 \ --emit-ref-confidence GVCF $ gatk GenotypeGVCFs \ --variant variants.g.vcf.gz \ --output variants.genotype.vcf.gz \ --reference genome.fa $ gatk VariantFiltration \ --reference genome.fa \ --variant variants.genotype.vcf.gz \ --output variants.filter.genotype.vcf.gz \ --filter-expression "QD < 5.0 || FS > 50.0 || SOR > 3.0 || MQ < 50.0 || MQRankSum < -2.5 || ReadPosRankSum < -1.0 || ReadPosRankSum > 3.5" \ --filter-name "FILTER" $ gatk SelectVariants \ --reference genome.fa \ --variant variants.filter.genotype.vcf.gz \ --output variants.varonly.vcf.gz \ --exclude-filtered \ --select-type-to-include SNP \ --select-type-to-include INDEL
$ java -jar snpEff.jar build -gtf22 -v RAP_MSU_on_IRGSP-1.0 $ java -jar snpEff.jar \ -v RAP_MSU_on_IRGSP-1.0 variants.varonly.vcf.gz | gzip -c > variants.snpEff.varonly.vcf.gz
*Reference genome sequence (FASTA), gene annotation data (GTF) and protein sequences of all genes (FASTA) should be placed in appropriate directories before running SnpEff.
$ perl tasuke_bamtodepth.pl \ -s samtools -c chromosome_list.csv -i alignment.rmdup.bam \ -o alignment_depth.tsv
The following two output files are uploaded to the TASUKE+ database
- variants.snpEff.varonly.vcf.gz
- alignment_depth.tsv
Information of rice accessions and sequence data provided in TASUKE+ of RAP-DB
ID (BioSample) | Name | Sub variety | Type | Origin | Reference | DOI | Avr. depth of coverage |
---|---|---|---|---|---|---|---|
SAMN02231725 | 93-11 | IND | Elite | China | Gao Z-U et al. 2013 | DOI: 10.1073/pnas.1306579110 | 42.55 |
SAMN02821253 | 175-1-127 | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 25.04 |
SAMN00027406 | Ai-Chiao-Hong | IND | Landrace | China | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.90 |
SAMD00045866 | Aichi Asahi 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.66 |
SAMD00045867 | Aichi Asahi 2 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.55 |
SAMEA104469242 | Aigansazhima | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 108.37 |
SAMD00045868 | Aikoku | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.52 |
SAMD00045869 | Aiyama | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.06 |
SAMD00045870 | Akage | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.96 |
SAMD00045871 | Akamai 2 | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.91 |
SAMD00045872 | Akebono | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.11 |
SAMD00080139 | Akidawara | TEJ | Elite | Japan | Ogawa D et al. 2018 | DOI: 10.1038/s41598-018-22657-3 | 33.74 |
SAMD00045874 | Akitakomachi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.15 |
SAMD00045875 | Akitsuho | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.58 |
SAMN00027400 | Arias | TRJ | Landrace | Indonesia (West Java) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 14.56 |
SAMEA3927580 | Arroz da Terra | JP | Elite | Portugal | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 13.28 |
SAMD00045876 | Asahi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.24 |
SAMD00045877 | Asahi Mochi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.52 |
SAMD00045878 | Asominori | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.72 |
SAMN00027396 | AZUCENA | TRJ | Landrace | Philippines | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.35 |
SAMN00027411 | BADAL 89 | JP/IND | Landrace | Bangladesh | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.33 |
SAMN02375091 | Badari Dhan | IND | Landrace | Nepal | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 16.79 |
SAMEA3927582 | Bahia | JP | Elite | Spain | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 12.73 |
SAMEA104469235 | Bairizao-4 | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 21.39 |
SAMEA104467892 | Bangbanggu | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 30.42 |
SAMEA104467888 | Basmati Surkh 89-15 | ARO | Elite | Pakistan | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 171.00 |
SAMD00078853 | Bei Khe | IND | Landrace | Cambodia | Itoh H et al. 2018 | DOI: 10.1111/tpj.13906 | 42.09 |
SAMD00080140 | Bekogonomi | TEJ | Elite | Japan | Ogawa D et al. 2018 | DOI: 10.1038/s41598-018-22657-3 | 22.98 |
SAMN07767782 | Bengal | TRJ | Elite | USA | Chai C et al. 2018 | DOI: 10.1038/s41598-018-32513-z | 26.16 |
SAMN02821220 | Bengal | TEJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 3.12 |
SAMD00045879 | Benkei | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.33 |
SAMN00027398 | Bico Branco | ARO | Elite | Brazil | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.80 |
SAMN00027390 | Binulawan | TRJ | Landrace | Philippines | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.76 |
SAMEA104469231 | Binxianludao | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 50.49 |
SAMEA2017052 | BLB | JP | Anther culture line | Korea | Jeong I-S et al. 2013 | DOI: 10.1186/1939-8433-6-6 | 45.14 |
SAMEA3927586 | Bomba | JP | Landrace | Spain | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 13.23 |
SAMN02821221 | Bowman | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 6.06 |
SAMD00066624 | C9285 | IND | Landrace | Bangladesh | Nagoya University | None | 16.48 |
SAMN00027418 | CA 97-053 | NIV | Wild | Cambodia (Sopoir Tep) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 14.40 |
SAMN02821254 | Camponi | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 11.40 |
SAMN00027405 | Canella DeFerro | TRJ | Elite | Brazil | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 17.13 |
SAMN02821222 | CarolinaGold | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 23.10 |
SAMN02821223 | CarolinaGoldSelect | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 37.45 |
SAMN02821224 | Catahoula | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 14.03 |
SAMN03273435 | CDR22 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 23.46 |
SAMN02869663 | CHANDINA | JP | Unknown | Sri lanka | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 15.74 |
SAMEA104469244 | Changlijingzhan | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 47.91 |
SAMEA104460755 | Changmadao-3 | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 20.07 |
SAMN03273436 | Chenghui047 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 23.32 |
SAMN00027408 | Chodongji | TEJ | Landrace | South Korea | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 16.00 |
SAMN03273446 | Chuannong422 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 20.24 |
SAMD00045880 | Chukyo Asahi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.03 |
SAMN02821225 | CL111 | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 11.28 |
SAMN02821226 | CL131 | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 15.48 |
SAMN02821227 | CL152 | TEJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 12.67 |
SAMN02821228 | CL261 | TEJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 10.79 |
SAMN02821229 | CMS08A | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 11.72 |
SAMN02821230 | CMS08B | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 9.40 |
SAMN04275173 | CO 39 | IND | Elite | India | Mahesh H. B. et al. 2016 | DOI: 10.1186/s12864-016-2523-7 | 142.89 |
SAMN02821231 | Cocodrie | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 10.21 |
SAMN02821255 | CT18685 | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 10.06 |
SAMN02821256 | CT19021-3-4-1V1-1 | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 24.82 |
SAMN02821257 | CT21375-F4-43-1 | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 24.62 |
SAMN02821258 | Curinga | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 12.60 |
SAMN02821232 | Cypress2 | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 6.44 |
SAMEA104469238 | Dabainuo | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 38.42 |
SAMD00045882 | Dango | TEJ | Unknown | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.24 |
SAMEA104467886 | Daohuaxiang 2 | TEJ | Elite | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 94.50 |
SAMN00027391 | Darmali | TEJ | Landrace | Nepal | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 11.01 |
SAMN00027416 | Davao | TRJ | Landrace | Philippines | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 13.15 |
SAMN03273427 | Dee geo woo gen | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 23.22 |
SAMN02375099 | Deejiaohualuo | IND | Unknown | China | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 15.01 |
SAMN02821233 | Della2 | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 14.00 |
SAMN06620501 | Digu | IND | Unknown | China | Li W et al. 2017 | DOI: 10.1016/j.cell.2017.06.008 | 22.24 |
SAMEA104460759 | Dishuigu | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 63.57 |
SAMN02821234 | Dixiebelle | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 34.81 |
SAMN01125970 | DJ123 | AUS | Elite | Bangladesh | Schatz MC et al. 2014 | DOI: 10.1186/s13059-014-0506-z | 143.90 |
SAMEA104469216 | DNJ 126 | AUS | Landrace | Bengal | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 64.74 |
SAMN02869652 | Dom Sufid | IND | Unknown | Iran | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 108.87 |
SAMEA2015633 | Dongjin | JP | Elite | Korea | Jeong I-S et al. 2013 | DOI: 10.1186/1939-8433-6-6 | 45.36 |
SAMEA104469240 | Dongying-8 | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 44.36 |
SAMD00045884 | Dontokoi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.98 |
SAMN02375107 | Dunghan Shali | JP | Unknown | Hungary | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 5.36 |
SAMN00027417 | DZ78 | AUS | Landrace | Bangladesh | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 16.70 |
SAMN02821259 | Esperanza | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 7.66 |
SAMN02821260 | Fanny | TEJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 23.08 |
SAMN02821261 | Fedearroz174 | IND | Elite | Latin America | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 8.79 |
SAMN02821262 | Fedearroz2000 | IND | Elite | Latin America | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 11.36 |
SAMN02821263 | Fedearroz50 | IND | Elite | Latin America | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 10.87 |
SAMEA104467891 | Fengrunhandaozi | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 76.19 |
SAMN00027425 | Firooz | ARO | Landrace | Iran | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 16.49 |
SAMN02821235 | Francis | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 3.72 |
SAMN03273437 | Fuhui838 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 20.65 |
SAMD00045885 | Fujisaka 5 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.18 |
SAMD00045886 | Fukoku | TEJ | Elite | Japan (Hokkaido) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.29 |
SAMD00045887 | Fukuhikari | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.22 |
SAMD00045888 | Fukunohana | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.14 |
SAMD00045889 | Funaki Omachi | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.40 |
SAMD00045890 | Futaba | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.62 |
SAMD00077985 | Genkitsukushi | TEJ | Elite | Japan | NICS | None | 58.29 |
SAMN00027415 | Gie 57 | IND | Landrace | Vietnam | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.86 |
SAMEA3927592 | Gigante Vercelli | JP | Elite | Italy | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 11.33 |
SAMD00045891 | Gin No Sei | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.70 |
SAMD00045892 | Gin No Yume | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.01 |
SAMD00045893 | Gin Oumi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.16 |
SAMD00045894 | Ginbouzu | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.66 |
SAMD00045895 | Ginbouzu7572 | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.26 |
SAMD00045896 | Ginginga | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.51 |
SAMEA3927587 | Gleva | JP | Elite | Spain | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 12.94 |
SAMD00010635 | Gohyakumangoku | TEJ | Elite | Japan | Arai-Kichise Y et al. 2014 | DOI: 10.1371/journal.pone.0086312 | 51.13 |
SAMD00045897 | Gohyakumangoku | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.01 |
SAMD00045898 | Goriki | TEJ | Landrace | Japan (Tottori) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.98 |
SAMN00027401 | Gotak Gatik | TRJ | Landrace | Indonesia (C.Java) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 12.76 |
SAMN00027407 | Guan-Yin-Tsan | IND | Landrace | China | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.78 |
SAMN03273447 | Guangchang13 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.00 |
SAMEA104467887 | Guangluai 4 | IND | Elite | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 149.84 |
SAMEA966194 | Guangluai-4 | IND | Elite | China | Huang X et al. 2010 | DOI: 10.1038/ng.695 | 17.09 |
SAMN03273433 | GUI630 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.53 |
SAMEA104469239 | Guihuanuo | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 49.23 |
SAMN02869654 | GURULEY | IND | Unknown | Bhutan | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 114.31 |
SAMN03879968 | Habun 1 | IND | Landrace | Taiwan | Wei FJ et al. 2016 | DOI: 10.1016/j.plantsci.2015.09.005 | 14.68 |
SAMN00027388 | Haginomae Mochi | TEJ | Elite | Japan | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 17.02 |
SAMN00027409 | HAISHA CAMAN | JP/IND | Landrace | Bangladesh | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 13.84 |
SAMD00045899 | Hanafubuki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.23 |
SAMN03273438 | Hanghui570 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 21.99 |
SAMD00045900 | Hatsu Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 6.28 |
SAMD00045905 | Hatsugozen | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.48 |
SAMD00045901 | Hattan 35 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.61 |
SAMD00045902 | Hattan Nishiki 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.14 |
SAMD00045903 | Hattan Nishiki 2 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.79 |
SAMD00045904 | Hattansou | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 8.08 |
SAMD00078858 | Hayamasari | TEJ | Elite | Japan | Itoh H et al. 2018 | DOI: 10.1111/tpj.13906 | 52.07 |
SAMD00045906 | Hayaoozeki 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.52 |
SAMN02821236 | Hidalgo | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 35.84 |
SAMD00045907 | Himenomochi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.26 |
SAMD00077984 | Hinohikari | TEJ | Elite | Japan | NICS | None | 53.03 |
SAMD00045908 | Hinohikari | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.21 |
SAMD00045909 | Hinomaru | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.19 |
SAMD00045910 | Hitachi Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.89 |
SAMN02375104 | Hitomebore | TEJ | Elite | Japan | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 27.62 |
SAMD00077981 | Hitomebore | TEJ | Elite | Japan | NICS | None | 55.27 |
SAMD00013510 | Hitomebore | TEJ | Elite | Japan | Takagi H et al. 2015 | DOI: 10.1038/nbt.3188 | 34.79 |
SAMD00045911 | Hitomebore | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.83 |
SAMD00045912 | Hiyadachitou | TEJ | Landrace | Japan (Yamagatai) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.38 |
SAMN00027413 | HK 47 | NIV | Wild | India (Madhya Pradesh) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 13.98 |
SAMD00045913 | Hokuriku 12 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.66 |
SAMD00045914 | Hokuriku 20 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.31 |
SAMD00045915 | Hokuriku 52 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.80 |
SAMD00003730 | Hokuriku193 | IND | Elite | Japan | Yonemaru J et al. 2014 | DOI: 10.1186/1471-2164-15-346 | 37.92 |
SAMD00045916 | Hokushin 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.43 |
SAMN02375100 | Hong Cheuh Zai | IND | Unknown | China | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 13.18 |
SAMEA104469243 | Honggu-1 | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 73.77 |
SAMEA104460747 | Honghandao | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 34.83 |
SAMEA104469245 | Hongmangnuo | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 25.15 |
SAMD00077980 | Hoshinoyume | TEJ | Elite | Japan | NICS | None | 55.29 |
SAMD00045917 | Hosogara | TEJ | Landrace | Japan (Aomori) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.12 |
SAMD00045919 | Houmanshinden Ine | TEJ | Landrace | Japan (Kagoshimai) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.05 |
SAMN02401119 | HR-12 | IND | Elite | India | Mahesh H. B. et al. 2016 | DOI: 10.1186/s12864-016-2523-7 | 81.15 |
SAMEA104469232 | Huakemangnuo | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 112.51 |
SAMEA2017528 | Hwayeong | JP | Elite | Korea | Jeong I-S et al. 2013 | DOI: 10.1186/1939-8433-6-6 | 45.79 |
SAMEA2016954 | HY-04 | JP | Anther culture line | Korea | Jeong I-S et al. 2013 | DOI: 10.1186/1939-8433-6-6 | 47.63 |
SAMEA2017592 | HY-08 | JP | Anther culture line | Korea | Jeong I-S et al. 2013 | DOI: 10.1186/1939-8433-6-6 | 47.16 |
SAMD00045920 | Hyogo Kita Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.36 |
SAMD00045921 | Hyogo Omachi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.40 |
SAMD00045922 | Hyogo Yumenishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.11 |
SAMD00045923 | Hyokei Sake 18 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.62 |
SAMD00045924 | Hyoukei Ka 56 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.10 |
SAMD00045925 | Hyoukei Ka 62 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 6.02 |
SAMEA104469219 | IAC 25 | TRJ | Elite | Brazil | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 69.10 |
SAMN02821237 | IAC600 | TEJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 21.84 |
SAMD00045926 | Ipponjime | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.74 |
SAMEA104469217 | IR 2797-115-3 | IND | Elite | Philippines | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 77.54 |
SAMN00027393 | IR 36 | IND | Improve | Brazil | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 16.73 |
SAMEA104469229 | IR 9209-26-2 | IND | Elite | Philippines | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 79.03 |
SAMN03273443 | IR1544 | IND | Elite | Philippines | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.39 |
SAMN03273430 | IR20 | IND | Elite | Philippines | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.89 |
SAMN03273429 | IR24 | IND | Elite | Philippines | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.73 |
SAMN03273431 | IR26 | IND | Elite | Philippines | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 24.06 |
SAMN03273432 | IR30 | IND | Elite | Philippines | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 21.90 |
SAMN03273445 | IR36 | IND | Elite | Philippines | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 24.44 |
SAMN02821264 | IR64 | IND | Elite | Philippines | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 16.30 |
SAMN01121943 | IR64 | IND | Elite | Philippines | Schatz MC et al. 2014 | DOI: 10.1186/s13059-014-0506-z | 174.56 |
SAMN02179223 | IR8 | IND | Elite | Philippines | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 23.24 |
SAMN03273428 | IR8 | IND | Elite | Philippines | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.26 |
SAMN02209968 | IR8 | IND | Elite | Philippines | Kim B et al. 2014 | DOI: 10.1186/s12284-014-0022-5 | 34.94 |
SAMN02821265 | IRGA424 | IND | Elite | Brazil | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 11.20 |
SAMN02821266 | IRGA427 | IND | Elite | Brazil | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 26.49 |
SAMN02869653 | IRGC13793 | IND | Unknown | Brunel | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 13.11 |
SAMN02869661 | IRGC28275 | JP | Unknown | pakistan | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 8.45 |
SAMN02869662 | IRGC32298 | JP | Unknown | Iran | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 29.83 |
SAMN02869664 | IRGC3860 | JP | Unknown | philippines | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 11.80 |
SAMN02869650 | IRGC50409 | IND | Unknown | Brazil | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 93.12 |
SAMN02869665 | IRGC56350 | JP | Unknown | Senegal | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 27.02 |
SAMN02869655 | IRGC58267 | IND | Unknown | Afghanistan | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 27.46 |
SAMN02869666 | IRGC58398 | JP | Unknown | Brunel | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 108.53 |
SAMN02869667 | IRGC58716 | JP | Unknown | Bangladesh | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 107.22 |
SAMN02869651 | IRGC69559 | IND | Unknown | Egypt | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 82.94 |
SAMN02869656 | IRGC9505 | IND | Unknown | Iraq | Wang M et al. 2014 | DOI: 10.1038/ng.3044 | 93.57 |
SAMD00045927 | Ishijiro | TEJ | Landrace | Japan (Toyama) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.02 |
SAMEA3927601 | Italica Livorno | JP | Elite | Italy | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 12.03 |
SAMD00045928 | Iwai | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 6.15 |
SAMN02375106 | Iwatekko | TEJ | Elite | Japan | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 21.24 |
SAMN02375108 | Jaguary | TRJ | Unknown | Brazil | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 13.76 |
SAMN00027387 | Jambu | TRJ | Landrace | Indonesia | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 12.46 |
SAMN02821238 | Jasmine85 | IND | Elite | Philippines | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 3.97 |
SAMN02821239 | Jazzman | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 8.20 |
SAMN02821240 | Jazzman2 | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 9.34 |
SAMN00027419 | JC101 | ARO | Elite | India | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 14.07 |
SAMN00027420 | JC111 | ARO | Elite | India | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.33 |
SAMN00027422 | JC91 | IND | Elite | India | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 16.16 |
SAMN02375098 | Jena 035 | IND | Landrace | Nepal | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 11.52 |
SAMN00027410 | Jhona 349 | AUS | Landrace | India | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 12.91 |
SAMEA104469246 | Jinzhan | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 44.90 |
SAMD00045929 | Joushuu | TEJ | Landrace | Japan (Yamagatai) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 2.78 |
SAMN02821241 | Jupiter | TEJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 9.21 |
SAMD00045930 | Kabashiko | TEJ | Landrace | Japan (Miyazaki) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.88 |
SAMD00019084 | Kaijin | TEJ | Elite | Japan | Takagi H et al. 2015 | DOI: 10.1038/nbt.3188 | 24.86 |
SAMD00045931 | Kairyo Hattannagare | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.53 |
SAMD00045932 | Kairyo Omachi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.55 |
SAMD00045933 | Kairyo Shinkou | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.55 |
SAMN00027404 | Kalamkati | AUS | Landrace | India | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 16.03 |
SAMEA3927594 | Kalao | JP | Elite | France | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 12.45 |
SAMN02375092 | Kaluheenati | IND | Landrace | Sri Lanka | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 13.73 |
SAMD00010636 | Kameji | TEJ | Landrace | Japan (Shimane) | Arai-Kichise Y et al. 2014 | DOI: 10.1371/journal.pone.0086312 | 44.20 |
SAMN03464928 | Kameji | TEJ | Landrace | Japan (Shimane) | Wei FJ et al. 2016 | DOI: 10.1016/j.plantsci.2015.09.005 | 14.92 |
SAMD00045934 | Kameji | TEJ | Landrace | Japan (Shimane) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.45 |
SAMD00045935 | Kamenoo | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.00 |
SAMD00045936 | Kamenoo 4 | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.94 |
SAMD00045937 | Kannomai | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.79 |
SAMN02375093 | Kasalath | IND | Landrace | India | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 10.77 |
SAMD00077988 | Kasalath | AUS | Landrace | India | NICS | None | 57.79 |
SAMD00016340 | Kasalath | AUS | Landrace | India | Sakai et al. 2014 | DOI: 10.1093/dnares/dsu006 | 24.42 |
SAMD00004056 | Kasalath | AUS | Landrace | India | Sakai et al. 2014 | DOI: 10.1093/dnares/dsu006 | 91.44 |
SAMEA104460752 | Kasalath | AUS | Landrace | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 182.85 |
SAMEA104469222 | Kbarai Ganja | AUS | Landrace | Pakistan | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 47.37 |
SAMN02375101 | Keiboba | IND | Landrace | China | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 11.02 |
SAMD00078857 | Khao Nam Jen | TRJ | Landrace | Laos | Itoh H et al. 2018 | DOI: 10.1111/tpj.13906 | 48.35 |
SAMD00078856 | Khau Mac Kho | TRJ | Landrace | Vietnam | Itoh H et al. 2018 | DOI: 10.1111/tpj.13906 | 58.57 |
SAMD00045938 | Kikusui 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.79 |
SAMD00045939 | Kinai Omachi | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.57 |
SAMD00045940 | Kinchaku | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.71 |
SAMD00045941 | Kinki 33 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.41 |
SAMD00045942 | Kinmaze | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 19.41 |
SAMD00045943 | Kinmon Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.40 |
SAMD00016906 | Kitaake | TEJ | Elite | Japan | Fujino K et al. 2015 | DOI: 10.1007/s00122-015-2543-8 | 32.87 |
SAMN00027385 | Kitrana 508 | ARO | Elite | Madagascar | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 16.72 |
SAMD00045944 | Koiomachi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.26 |
SAMD00045945 | Kojyou Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.34 |
SAMD00045946 | Kokuryomiyako | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.67 |
SAMEA104459806 | Kongyu 131 | TEJ | Elite | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 106.33 |
SAMD00010632 | Koshihikari | TEJ | Elite | Japan | Arai-Kichise Y et al. 2014 | DOI: 10.1371/journal.pone.0086312 | 51.07 |
SAMD00077979 | Koshihikari | TEJ | Elite | Japan | NICS | None | 54.49 |
SAMD00045947 | Koshihikari | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 95.50 |
SAMEA104460751 | Koshihikari | TEJ | Elite | Japan | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 108.81 |
SAMD00077986 | Koshihikari SBL1 | TEJ | Elite | Japan | NICS | None | 56.45 |
SAMN00027394 | KUI SALI | ARO | Landrace | Bangladesh | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 14.79 |
SAMD00045950 | Kuranohana | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.38 |
SAMD00045951 | Kyoto Asahi | TEJ | Landrace | Japan (Kyoto) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.34 |
SAMD00045952 | Kyoutoasahi | TEJ | Landrace | Japan (Kyoto) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.73 |
SAMN00027382 | L 89-12 | NIV | Wild | Laos (Vientiane) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.49 |
SAMN02821242 | L-201 | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 3.81 |
SAMEA3927598 | L202 | JP | Elite | USA | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 13.02 |
SAMN02821267 | L2825-CA | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 12.44 |
SAMN02821243 | LA2177 | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 10.66 |
SAMD00078855 | LAC 23 | TRJ | Unknown | Nigeria | Itoh H et al. 2018 | DOI: 10.1111/tpj.13906 | 43.00 |
SAMN02821244 | Lagrue3 | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 5.05 |
SAMN02821245 | Lemont | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 4.48 |
SAMN00027412 | Lemont | TRJ | Elite | USA (TX) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 13.27 |
SAMEA104469236 | Lengshuizhan | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 25.73 |
SAMN00027392 | Leung Pratew | IND | Landrace | Thailand | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 14.64 |
SAMN02821246 | LM-1 | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 3.74 |
SAMEA104460749 | Longgeng 31 | TEJ | Elite | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 96.74 |
SAMEA3927602 | Loto | JP | Elite | Italy | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 11.83 |
SAMEA3927607 | LTH | JP | Elite | China | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 12.71 |
SAMN03273448 | Luchang-3 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 20.82 |
SAMEA104469249 | Luyu132-1 | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 24.85 |
SAMEA3927608 | M202 | JP | Elite | USA | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 11.50 |
SAMEA104469237 | Maguhongmi | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 61.30 |
SAMN00027383 | Maintmolotsy | TRJ | Elite | Madagascar | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 12.56 |
SAMD00045953 | Mangoku | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.71 |
SAMN00027414 | Mansaku | TEJ | Landrace | Japan | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.66 |
SAMD00045954 | Mansaku | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.45 |
SAMN02821247 | MCR010277 | ADMIX | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 3.71 |
SAMN00027386 | Mehr | AUS | Landrace | Iran | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.72 |
SAMN02821248 | Mermentau | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 10.59 |
SAMN03273440 | Mianhui725 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 23.81 |
SAMEA104469228 | Milyang84 | TEJ | Elite | North Korea | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 56.00 |
SAMEA104469221 | Minanok (glut) | TRJ | Elite | Philippines | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 60.79 |
SAMN03273434 | Minghui63 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 21.73 |
SAMN03273439 | Minghui70 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 21.15 |
SAMN03273441 | Minghui86 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.69 |
SAMN00027389 | Miriti | IND | Landrace | Bangladesh | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 12.68 |
SAMD00045955 | Misato Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.57 |
SAMD00045956 | Miyama Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.63 |
SAMD00003727 | Mizuhochikara | JP/IND | Elite | Japan | Yonemaru J et al. 2014 | DOI: 10.1186/1471-2164-15-346 | 35.54 |
SAMD00045957 | Morita Wase | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.54 |
SAMD00010631 | Moroberekan | TRJ | Landrace | Guinea | Arai-Kichise Y et al. 2014 | DOI: 10.1371/journal.pone.0086312 | 38.72 |
SAMN03879965 | Muteka | TEJ | Landrace | Taiwan | Wei FJ et al. 2016 | DOI: 10.1016/j.plantsci.2015.09.005 | 13.86 |
SAMEA104467889 | Mutiara | TRJ | Elite | Indonesia | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 92.26 |
SAMD00045958 | Mutsuhomare | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.19 |
SAMN00027381 | MV 89-80 | NIV | Wild | India (Medinipur) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.32 |
SAMD00045959 | Nada Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.44 |
SAMD00045960 | Nadahikari | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.21 |
SAMD00045961 | Nagoya Shiro | TEJ | Landrace | Japan (Akita) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.89 |
SAMN03879967 | Nakabo | TEJ | Landrace | Taiwan | Wei FJ et al. 2016 | DOI: 10.1016/j.plantsci.2015.09.005 | 13.12 |
SAMD00045962 | Nakate Shinriki | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.08 |
SAMD00045963 | Nakate Shinsenbon | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.67 |
SAMN03273449 | Nante | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 21.19 |
SAMN02375112 | NERICA 1 | JP/GLA | Elite | Africa | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 12.09 |
SAMD00116538 | NERICA 3 | TRJ/GLA | Elite | Africa | Yamamoto N et al. 2018 | DOI: 10.1186/s12284-018-0224-3 | 41.10 |
SAMD00116539 | NERICA 4 | TRJ/GLA | Elite | Africa | Yamamoto N et al. 2018 | DOI: 10.1186/s12284-018-0224-3 | 55.42 |
SAMD00116540 | NERICA 5 | TRJ/GLA | Elite | Africa | Yamamoto N et al. 2018 | DOI: 10.1186/s12284-018-0224-3 | 64.00 |
SAMD00116541 | NERICA 7 | TRJ/GLA | Elite | Africa | Yamamoto N et al. 2018 | DOI: 10.1186/s12284-018-0224-3 | 47.05 |
SAMD00045964 | Nihonmasari | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.73 |
SAMN02375103 | Nipponbare | TEJ | Elite | Japan | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 19.52 |
SAMD00077987 | Nipponbare | TEJ | Elite | Japan | NICS | None | 51.41 |
SAMN00139534 | Nipponbare | TEJ | Elite | Japan | Schatz MC et al. 2014 | DOI: 10.1186/s13059-014-0506-z | 114.38 |
SAMN00027423 | Nipponbare | TEJ | Elite | Japan | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 11.37 |
SAMD00045965 | Nipponbare | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 91.68 |
SAMEA104469250 | Nipponbare | TEJ | Elite | Japan | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 69.47 |
SAMD00045966 | Nojyouho | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.04 |
SAMN07767800 | Nona Bokra | IND | Landrace | India | Chai C et al. 2018 | DOI: 10.1038/s41598-018-32513-z | 15.84 |
SAMD00078854 | Nona Bokra | IND | Landrace | India | Itoh H et al. 2018 | DOI: 10.1111/tpj.13906 | 37.60 |
SAMEA871359 | Nongken-58 | TEJ | Elite | Japan | Huang X et al. 2010 | DOI: 10.1038/ng.695 | 11.57 |
SAMEA104469223 | Nonglinnuo-144 | TEJ | Elite | Japan | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 45.33 |
SAMD00045967 | Norin 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.39 |
SAMD00045968 | Norin 17 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.69 |
SAMN00027399 | Norin 20 | TEJ | Landrace | Japan | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 14.88 |
SAMD00045969 | Norin 21 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.87 |
SAMD00045970 | Norin 22 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.47 |
SAMD00045971 | Norin 41 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.13 |
SAMD00045972 | Norin 8 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.65 |
SAMD00010634 | Norin8 | TEJ | Elite | Japan | Arai-Kichise Y et al. 2014 | DOI: 10.1371/journal.pone.0086312 | 63.63 |
SAMN00027397 | NPE 844 | TRJ | Landrace | Pakistan | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 16.83 |
SAMN03263070 | O. barthii (IRGC101252) | BAR | Wild | Burkina Faso | Zhang Q-J et al. 2014 | DOI: 10.1073/pnas.1418307111 | 37.02 |
SAMN02941239 | O. barthii (IRGC105608) | BAR | Wild | Africa | Stein JC et al. 2018 | DOI:10.1038/s41588-018-0040-0 | 109.37 |
SAMD00116543 | O. glaberrima (CG14) | GLA | Elite | Africa | Yamamoto N et al. 2018 | DOI: 10.1186/s12284-018-0224-3 | 51.05 |
SAMN03263068 | O. glaberrima (IRGC103486) | GLA | Landrace | Ivory Coast | Zhang Q-J et al. 2014 | DOI: 10.1073/pnas.1418307111 | 50.13 |
SAMN02941241 | O. glumaepatula (GEN1233) | GLU | Wild | USA | Stein JC et al. 2018 | DOI:10.1038/s41588-018-0040-0 | 73.86 |
SAMN03263071 | O. glumaepatula (IRGC88793) | GLU | Wild | Brazil | Zhang Q-J et al. 2014 | DOI: 10.1073/pnas.1418307111 | 71.17 |
SAMD00003589 | O. longistaminata (W1413) | LON | Wild | Sierra Leone | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 10.51 |
SAMD00003590 | O. longistaminata (W1508) | LON | Wild | Madagascar | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 6.74 |
SAMN03263073 | O. meridionalis (IRGC105298) | MER | Wild | Australia | Zhang Q-J et al. 2014 | DOI: 10.1073/pnas.1418307111 | 39.29 |
SAMN02870169 | O. meridionalis (OR44/W2112) | MER | Wild | Australia | Stein JC et al. 2018 | DOI:10.1038/s41588-018-0040-0 | 92.27 |
SAMN00027378 | O. nivara (042/87/34) | NIV | Wild | India (Dhoni) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.38 |
SAMN02941243 | O. nivara (IRGC100897) | NIV | Wild | India | Stein JC et al. 2018 | DOI:10.1038/s41588-018-0040-0 | 85.94 |
SAMN03263067 | O. nivara (IRGC88812) | NIV | Wild | Laos | Zhang Q-J et al. 2014 | DOI: 10.1073/pnas.1418307111 | 6.75 |
SAMN02941238 | O. punctata (IRGC105690) | PUN | Wild | Africa | Stein JC et al. 2018 | DOI:10.1038/s41588-018-0040-0 | 75.30 |
SAMN00027380 | O. rufipogon (DAL DHAN) | RUF | Wild | Bangladesh (Chakaria) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.63 |
SAMN00027424 | O. rufipogon (P46) | RUF | Wild | China (Hainan) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 13.05 |
SAMN00027379 | O. rufipogon (PADI PADIAN) | RUF | Wild | Indonesia (Kromat Watu) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.42 |
SAMN00027426 | O. rufipogon (VOC4) | RUF | Wild | Nepal | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 14.72 |
SAMD00016753 | O. rufipogon (W0106) | RUF | Wild (Or-I) | India | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 9.63 |
SAMN02375087 | O. rufipogon (W0120) | RUF | Wild | India | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 21.95 |
SAMD00004173 | O. rufipogon (W0120) | RUF | Wild (Or-II) | India | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 29.06 |
SAMEA104459802 | O. rufipogon (W0123-1) | RUF | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 41.54 |
SAMEA104469252 | O. rufipogon (W0141) | RUF | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 69.88 |
SAMEA104469253 | O. rufipogon (W0170) | RUF | Wild | Thailand | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 70.86 |
SAMD00004178 | O. rufipogon (W0180) | RUF | Wild (Or-II) | Thailand | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 25.97 |
SAMD00004175 | O. rufipogon (W0593) | RUF | Wild (Or-III) | Malaya | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 29.69 |
SAMD00004172 | O. rufipogon (W0630) | RUF | Wild (Or-I) | Burma | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 33.62 |
SAMD00004177 | O. rufipogon (W1230) | RUF | Wild (Or-I) | Dutch New Guinea | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 28.93 |
SAMD00004176 | O. rufipogon (W1236) | RUF | Wild (Or-II) | Australian New Guinea | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 29.96 |
SAMN03273454 | O. rufipogon (W1543) | RUF | Wild | Unknown | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.87 |
SAMEA104469254 | O. rufipogon (W1687) | RUF | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 57.75 |
SAMEA104469255 | O. rufipogon (W1698) | RUF | Wild | Thailand | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 56.41 |
SAMD00004174 | O. rufipogon (W1715) | RUF | Wild (Or-II) | China | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 23.48 |
SAMEA104469256 | O. rufipogon (W1739) | RUF | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 91.69 |
SAMEA104469257 | O. rufipogon (W1754) | RUF | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 93.74 |
SAMEA104469258 | O. rufipogon (W1777) | RUF | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 81.49 |
SAMN02375083 | O. rufipogon (W1807) | RUF | Wild | Sri Lanka | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 18.96 |
SAMN02375089 | O. rufipogon (W1886) | RUF | Wild | Thailand | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 20.37 |
SAMD00016754 | O. rufipogon (W1921) | RUF | Wild (Or-I) | Thailand | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 8.89 |
SAMEA1523624 | O. rufipogon (W1943) | RUF | Wild (Or-III) | China | Stein JC et al. 2018 | DOI:10.1038/s41588-018-0040-0 | 15.60 |
SAMEA104469259 | O. rufipogon (W1943) | RUF | Wild | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 152.52 |
SAMN02375090 | O. rufipogon (W1965) | RUF | Wild | China | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 24.33 |
SAMN02375085 | O. rufipogon (W1976) | RUF | Wild | Indonesia | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 22.03 |
SAMEA104469260 | O. rufipogon (W1979) | RUF | Wild | Indonesia | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 62.08 |
SAMD00004179 | O. rufipogon (W1981) | RUF | Wild (Or-II) | Indonesia | Ohyanagi et al. 2016 | DOI: 10.1093/pcp/pcv171 | 28.89 |
SAMN02375084 | O. rufipogon (W2003) | RUF | Wild | India | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 19.75 |
SAMEA104469261 | O. rufipogon (W2012) | RUF | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 108.27 |
SAMN02375086 | O. rufipogon (W2057) | RUF | Wild | Bangladesh | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 24.75 |
SAMEA104459805 | O. rufipogon (W3078-2) | RUF | Wild | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 89.83 |
SAMEA104459804 | O. rufipogon (W3095-2) | RUF | Wild | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 85.60 |
SAMN02375081 | O. rufipogon (W593) | RUF | Wild | Malaysia | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 32.71 |
SAMN02375088 | O. rufipogon (W630) | RUF | Wild | Myammar | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 32.24 |
SAMD00045974 | Okayama Yakusake 48 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.66 |
SAMD00009825 | Omachi | TEJ | Landrace | Japan (Okayama) | Arai-Kichise Y et al. 2011 | DOI: 10.1093/pcp/pcr003 | 48.56 |
SAMD00045978 | Omachi_1 | TEJ | Landrace | Japan (Okayama) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 8.45 |
SAMD00045977 | Omachi_2 | TEJ | Landrace | Japan (Okayama) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.22 |
SAMN02821268 | Oryzica 3 | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 12.23 |
SAMN02821269 | Oryzica Llanos 5 | IND | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 11.67 |
SAMD00045979 | Oseto | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.17 |
SAMD00045975 | Ouu 2 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.10 |
SAMD00045980 | Ouu 237 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.89 |
SAMD00045981 | Ouu 239 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.55 |
SAMD00045982 | Oyama Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.45 |
SAMEA104469224 | Pama | TEJ | Elite | Philippines | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 71.66 |
SAMN02821270 | Parao | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 30.02 |
SAMEA3927613 | Pavlovsky | JP | Elite | Russia | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 10.88 |
SAMN00027395 | Phudugey | TEJ | Landrace | Bhutan | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 15.26 |
SAMN02821271 | Pionero2010FL | IND | Elite | Venezuela | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 20.83 |
SAMN03273426 | Pitai | IND | Elite | Indonesia | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.12 |
SAMN00027402 | Popot 165 | IND | Landrace | Indonesia (E.Kalimantan) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 14.99 |
SAMN07767773 | PSRR-1 | WEEDY | Weedy | USA | Chai C et al. 2018 | DOI: 10.1038/s41598-018-32513-z | 33.93 |
SAMEA3927615 | Puntal | JP | Elite | Spain | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 13.41 |
SAMN04442258 | Purple puttu | IND | Landrace | India | Lachagari V. B. R et al. 2019 | DOI: 10.3389/fpls.2019.00513 | 96.16 |
SAMEA104469233 | Qiananshuinuo | TEJ | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 86.23 |
SAMD00045983 | Raiden | TEJ | Landrace | Japan (Kanto Higashiyama) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 6.43 |
SAMN02375094 | Ratul | IND | Landrace | India | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 16.05 |
SAMD00045984 | Reihou | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.18 |
SAMD00045985 | Reimei | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.00 |
SAMN02375110 | Rexmont | TRJ | Elite | United States | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 14.94 |
SAMD00045987 | Rikutou Rikuu 2 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.07 |
SAMD00045986 | Rikuu 132 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.77 |
SAMD00045988 | Rokko Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.26 |
SAMN03751782 | RP Bio-226 | IND | Elite | India | Reddy M M et al. 2015 | DOI: 10.3389/fpls.2015.00896 | 24.13 |
SAMEA104469234 | Ruanzhanjiugu | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 26.66 |
SAMD00080141 | Ruriaoba | IND | Elite | Japan | Ogawa D et al. 2018 | DOI: 10.1038/s41598-018-22657-3 | 38.50 |
SAMN02821249 | Saber | TRJ | Elite | Unknown | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 36.12 |
SAMD00045948 | Sachidama 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.73 |
SAMD00045949 | Sachidama 2 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.57 |
SAMD00045989 | Sachikaze | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.96 |
SAMD00045990 | Saga No Hana | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.80 |
SAMD00045991 | Saikai 134 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.56 |
SAMD00045992 | Sake Pikari | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.04 |
SAMN11233562 | Samgwang | TEJ | Elite | Korea | Kang D-Y et al. 2019 | DOI: 10.3390/ijms20102598 | 68.39 |
SAMD00045994 | Sasanishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.99 |
SAMN02375105 | Sasanishiki | TEJ | Elite | Japan | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 15.19 |
SAMD00045995 | Sasashigure | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.29 |
SAMN05200854 | Seeragasamba | IND | Landrace | India | Bindusree G et al. 2017 | DOI: 10.1371/journal.pone.0188920 | 7.20 |
SAMD00045996 | Sekikei 56 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.35 |
SAMD00045997 | Sekiyama | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.39 |
SAMD00045998 | Senbon Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.26 |
SAMEA3927619 | Senia | JP | Elite | Spain | Reig-Valiente JL et al. 2016 | DOI: 10.1186/s12284-016-0130-5 | 13.22 |
SAMN03273450 | Shenglixian | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.42 |
SAMD00046000 | Shichimenchou Mochi | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.26 |
SAMD00046001 | Shiga Wataribune 2 | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.95 |
SAMD00046002 | Shin Igou | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.74 |
SAMD00046003 | Shin Yamabuki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 2.74 |
SAMD00046005 | Shinjyu | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.08 |
SAMN03464929 | Shinriki | TEJ | Landrace | Japan (Hyogo) | Wei FJ et al. 2016 | DOI: 10.1016/j.plantsci.2015.09.005 | 17.56 |
SAMD00046006 | Shinriki | TEJ | Landrace | Japan (Hyogo) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 6.73 |
SAMD00046007 | Shinriki Mochi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.35 |
SAMD00046008 | Shinshuu | TEJ | Landrace | Japan (Nagano) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.57 |
SAMD00046004 | Shinyamadaho 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.86 |
SAMD00046009 | Shinyamadaho 2 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.05 |
SAMD00046010 | Shiragiku | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.36 |
SAMD00046011 | Shirakaba Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.32 |
SAMD00046012 | Shirayukihime | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.81 |
SAMD00046013 | Shiroine | TEJ | Landrace | Japan (Tokushima) | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.06 |
SAMD00046014 | Shirosenbon | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.06 |
SAMD00046015 | Shirotae Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.19 |
SAMN02375095 | Shoni | IND | Landrace | Bangladesh | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 13.08 |
SAMN02821250 | ShuFeng | IND | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 3.46 |
SAMD00046017 | Shuhou | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 2.56 |
SAMN03273444 | Shuhui527 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 20.04 |
SAMEA104469247 | Shuihegu | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 40.67 |
SAMD00046016 | Siranui | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.98 |
SAMEA104469241 | Sizhan | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 50.00 |
SAMN07426270 | Suijing18 | JP | Elite | China | Nie S et al. 2017 | DOI:10.1038/sdata.2017.195 | 52.81 |
SAMN02375096 | Surjmukhi | IND | Elite | India | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 16.45 |
SAMD00003728 | Suweon258 | IND | Elite | Korea | Yonemaru J et al. 2014 | DOI: 10.1186/1471-2164-15-346 | 37.24 |
SAMEA104469220 | T 480-34 | IND | Elite | Cuba | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 74.72 |
SAMN00027384 | Ta HungKu | TEJ | Landrace | China | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 12.41 |
SAMD00003726 | Tachiaoba | TEJ | Elite | Japan | Yonemaru J et al. 2014 | DOI: 10.1186/1471-2164-15-346 | 39.45 |
SAMD00003729 | Tachisugata | IND | Elite | Japan | Yonemaru J et al. 2014 | DOI: 10.1186/1471-2164-15-346 | 34.04 |
SAMN04275184 | Tadukan | IND | Landrace | Philippines | Mahesh H. B. et al. 2016 | DOI: 10.1186/s12864-016-2523-7 | 93.46 |
SAMN03463201 | Taichung 65 | TEJ | Elite | Taiwan | Wei FJ et al. 2016 | DOI: 10.1016/j.plantsci.2015.09.005 | 5.70 |
SAMN02209969 | Taichung Native 1 | IND | Elite | Taiwan | Kim B et al. 2014 | DOI: 10.1186/s12284-014-0022-5 | 34.44 |
SAMD00046018 | Tajima Goriki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 2.69 |
SAMN02375102 | Takanari | IND | Elite | Japan | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 9.30 |
SAMD00003725 | Takanari | IND | Elite | Japan | Yonemaru J et al. 2014 | DOI: 10.1186/1471-2164-15-346 | 34.33 |
SAMD00046019 | Takane Nishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.12 |
SAMD00046020 | Takenari 8043 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.81 |
SAMD00046021 | Tasensho | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.39 |
SAMN00027421 | TD2 | IND | Elite | Thailand | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 11.15 |
SAMEA104469226 | Tebonnet | TRJ | Elite | USA | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 99.18 |
SAMEA104469227 | Teng-870 | TEJ | Elite | Japan | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 56.52 |
SAMD00077983 | Tenkomori | TEJ | Elite | Japan | NICS | None | 54.57 |
SAMD00077982 | Tentakaku | TEJ | Elite | Japan | NICS | None | 55.25 |
SAMN02821251 | TeQing | IND | Elite | China | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 4.60 |
SAMN03273451 | Tetep | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 23.58 |
SAMN04275185 | Tetep | IND | Landrace | Vietnam | Mahesh H. B. et al. 2016 | DOI: 10.1186/s12864-016-2523-7 | 45.79 |
SAMD00046022 | Todorokiwase | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.23 |
SAMD00045881 | Togoh 1 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.47 |
SAMD00045918 | Togoh 2 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.76 |
SAMD00045973 | Togoh 3 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 2.97 |
SAMD00045976 | Togoh 4 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.86 |
SAMD00045873 | Togoh 5 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.06 |
SAMD00045999 | Togoh 6 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.43 |
SAMD00045883 | Togoh 7 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.16 |
SAMEA104460753 | Tohoku IL9 | TEJ | Elite | Japan | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 87.96 |
SAMN02209972 | Tongil | JP/IND | Elite | Korean | Kim B et al. 2014 | DOI: 10.1186/s12284-014-0022-5 | 45.81 |
SAMD00046026 | Tono 1 | TEJ | Unknown | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.11 |
SAMD00046027 | Tosanishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.10 |
SAMD00046023 | Toujinohana | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.36 |
SAMD00046024 | Toujinoyume | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.48 |
SAMD00046025 | Toukai Asahi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.50 |
SAMD00046028 | Toyonishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 7.90 |
SAMN00027403 | Trembese | TRJ | Landrace | Indonesia (East Java) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 12.76 |
SAMD00046029 | Tsuyubakaze | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 2.24 |
SAMD00078852 | Tupa 121-3 | IND | Landrace | Bangladesh | Itoh H et al. 2018 | DOI: 10.1111/tpj.13906 | 39.72 |
SAMN02375111 | Tupa 729 | TRJ | Landrace | Bangladesh | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 14.63 |
SAMN02375097 | Tupa121-3 | IND | Landrace | Bangladesh | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 12.84 |
SAMN02375109 | Urasan 1 | TRJ | Elite | Japan | Fawcett J et al. 2013 | DOI:10.1371/journal.pone.0083720 | 14.41 |
SAMEA104469251 | W0128 | IND | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 71.04 |
SAMEA104459803 | W3105-1 | AUS | Wild | India | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 145.70 |
SAMD00116542 | WAB 56-104 | TRJ | Elite | Africa | Yamamoto N et al. 2018 | DOI: 10.1186/s12284-018-0224-3 | 49.40 |
SAMD00046030 | Wakaba | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.05 |
SAMD00046031 | Wakamizu | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.37 |
SAMN03273442 | Wanhui88 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.28 |
SAMN03273452 | Wanlixian | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.31 |
SAMD00046032 | Wase Asahi | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 5.32 |
SAMD00046033 | Wase Shinriki | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.52 |
SAMD00046034 | Wataribune 1681 | TEJ | Landrace | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 2.67 |
SAMN02821252 | Wells | TRJ | Elite | USA | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 4.30 |
SAMEA104459807 | Wuyungeng 7 | TEJ | Elite | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 62.44 |
SAMEA104467890 | Xiangnan-1 | IND | Elite | North Korea | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 72.60 |
SAMD00046035 | Yamabiko | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.76 |
SAMD00046036 | Yamadaho 132 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 7.45 |
SAMD00010633 | Yamadanishiki | TEJ | Elite | Japan | Arai-Kichise Y et al. 2014 | DOI: 10.1371/journal.pone.0086312 | 38.77 |
SAMD00046037 | Yamadanishiki | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.47 |
SAMD00045993 | Yamasakae | TEJ | Unknown | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.53 |
SAMEA104469248 | Yanzhan | IND | Landrace | China | Zhao Q et al. 2018 | DOI: 10.1038/s41588-018-0041-z | 48.15 |
SAMN00027427 | Yuan3-9 | RUF | Wild | China (Yunnan) | Xu et al. 2011 | DOI: 10.1038/nbt.2050 | 11.71 |
SAMN02209992 | Yukara | JP | Elite | Japan | Kim B et al. 2014 | DOI: 10.1186/s12284-014-0022-5 | 37.96 |
SAMD00046038 | Yukigeshou | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.63 |
SAMD00046039 | Yumesansui | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 3.68 |
SAMN02821272 | Zafiro | TEJ | Elite | Chile | Duitama J et al. 2015 | DOI: 10.1371/journal.pone.0124617 | 7.19 |
SAMD00046040 | Zengokuwase | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 8.18 |
SAMD00046041 | Zensyo 26 | TEJ | Elite | Japan | Yano K et al. 2016 | DOI: 10.1038/ng.3596 | 4.50 |
SAMN03273453 | Zhongnong-4 | IND | Elite | China | Huang J et al. 2018 | DOI:10.1073/pnas.1806110115 | 22.05 |