Table 1 List of databases for rice genomics

Genome browser

Rice Genome Annotation Project

http://rice.plantbiology.msu.edu/

10.1186/1939-8433-6-4

○^a

850/2007

The Rice Annotation Project

https://rapdb.dna.affrc.go.jp/index.html

10.1093/nar/gkj094

○

237/2006

RiceGE

http://signal.salk.edu/cgi-bin/RiceGE

N/A^b

○

N/A/2004

RIGW

http://rice.hzau.edu.cn/rice/

10.1016/j.molp.2017.10.003

○

1/2017

RPAN

http://cgm.sjtu.edu.cn/3kricedb/

10.1093/nar/gkw958

○

17/2016

BGI-RIS

http://rise2.genomics.org.cn/page/rice/index.jsp

10.1093/nar/gkh085

N/A

119/2004

OryGenesDB

http://orygenesdb.cirad.fr/index.html

10.1093/nar/gkj012

○

78/2006

IC4

http://ic4r.org/

10.1093/nar/gkv1141

○

GWAS

RiceVarMap v2

http://ricevarmap.ncpgr.cn/v2

10.1093/nar/gku894

○

51/2014

SNP-Seek

http://snp-seek.irri.org/

10.1093/nar/gkw1135

○

18/2016

Oryzagenome

http://viewer.shigen.info/oryzagenome2detail/index.xhtml

10.1093/pcp/pcv171

○

107/2006

Ricebase

https://www.ricebase.org/

10.1093/database/baw107

○

9/2016

HapRice

http://qtaro.abr.affrc.go.jp/qsnp/snp

10.1093/pcp/pct188

○

27/2014

Rice imputation server

http://rice-impute.biotech.cornell.edu/

10.1038/s41467-018-05538-1

○

1/2018

iPat

http://zzlab.net/iPat/

10.1093/bioinformatics/bty015

○

0/2018

The GWAS viewer

http://rs-bt-mccouch4.biotech.cornell.edu/GWAS_Viewer/plot/

10.1038/ncomms10532

○

98/2016

Comparative Genomics

Gramene

http://www.gramene.org/

10.1093/nar/gkx1111

○

234/2002

Phytozome

https://phytozome.jgi.doe.gov/pz/portal.html

10.1093/nar/gkr944

○

1749/2011

Ensemble_rice

http://plants.ensembl.org/Oryza_sativa/Info/Index

10.1093/nar/gkx1011

○

41/2016

PLAZA

https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v4_monocots/

10.1093/nar/gkx1002

○

238/2009

PlantGDB

http://www.plantgdb.org/

10.1093/nar/gkm1041

○

174/2004