In this section

26 rice_cultivars Cactus

This alignment has been generated in Ensembl Plants release 57.

API access

This alignment set can be accessed using the Compara API via the Bio::EnsEMBL::DBSQL::MethodLinkSpeciesSetAdaptor using the method_link_type "CACTUS_HAL" and the species_set_name "collection-rice_cultivars".

HAL configuration

HAL alignments require further configuration. See the instructions in our README.

SpeciesAssemblyGenome length (bp)Genome coverage (bp)Genome coverage (%)
Oryza sativa Japonica GroupIRGSP-1.0375,049,285354,985,97094.65
Oryza sativa (Geng/Japonica-sbtrp var. Chao Meo) (Oryza sativa tropical japonica subgroup)Os132278RS1383,243,376362,020,14194.46
Oryza sativa (Geng/Japonica-trop1 var. Azucena) (Oryza sativa tropical japonica subgroup)AzucenaRS1381,570,127366,201,83795.97
Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka) (Oryza sativa tropical japonica subgroup)Os128077RS1382,007,384359,362,16294.07
Oryza sativa (circum-Basmati var. ARC 10497) (Oryza sativa aromatic subgroup)Os117425RS1380,354,188352,354,24992.64
Oryza sativa (circum-Aus2 var. Natel Boro) (Oryza sativa aus subgroup)Os127652RS1384,203,823354,158,27292.18
Oryza sativa (circum-Aus1 var. N22) (Oryza sativa aus subgroup)OsN22RS2388,175,468360,160,16392.78
Oryza sativa (Xian/Indica-adm var. Minghui 63) (Oryza sativa Indica Group)MH63RS2395,765,488375,616,87194.91
Oryza sativa (Xian/Indica-1B1 var. IR64) (Oryza sativa Indica Group)OsIR64RS1387,434,309364,974,61994.20
Oryza sativa (Xian/Indica-1B2 var. PR106) (Oryza sativa Indica Group)Os127742RS1394,601,903374,702,01094.96
Oryza sativa (Xian/Indica-3A var. Lima) (Oryza sativa Indica Group)Os127564RS1405,399,143376,462,00892.86
Oryza sativa (Xian/Indica-2A var. Gobol Sail) (Oryza sativa Indica Group)Os132424RS1392,847,014367,725,40993.61
Oryza sativa (Xian/Indica-3B1 var. Khao Yai Guang) (Oryza sativa Indica Group)Os127518RS1399,249,348374,579,58993.82
Oryza sativa (Xian/Indica-3B2 var. Liu Xu) (Oryza sativa Indica Group)Os125827RS1490,154,521441,968,17590.17
Oryza sativa (Xian/Indica-1A var. Zhenshan 97) (Oryza sativa Indica Group)ZS97RS3391,561,630368,635,62294.14
Oryza sativa (Xian/Indica-2B var. Larha Mugad) (Oryza sativa Indica Group)Os125619RS1391,869,645357,109,56091.13
Oryza nivara (Oryza sativa f. spontanea)Oryza_nivara_v1.0337,950,324303,025,24389.67
Oryza rufipogonOR_W1943338,040,714291,474,77286.22
Oryza barthiiO.barthii_v1308,272,304291,812,00194.66
Oryza glaberrimaOryza_glaberrima_V1316,419,574282,153,69089.17
Oryza glumipatulaOryza_glumaepatula_v1.5372,860,283275,087,17473.78
Oryza longistaminataO_longistaminata_v1.0326,442,508260,318,86379.74
Oryza meridionalisOryza_meridionalis_v1.3335,668,232216,335,73564.45
Oryza punctataOryza_punctata_v1.2393,816,603185,467,80847.09
Oryza brachyanthaOryza_brachyantha.v1.4b260,838,168120,153,83646.06
Leersia perrieriLperr_V1.4266,687,832122,967,44446.11

Cactus coverage calculation

Cactus coverage values are obtained from the output of halAlignmentDepth (Hickey et al. 2013), then aggregated per genome.