GeneCAD GFF resource
Gene annotations predicted with GeneCAD for plant genomes and for the maize NAM founder lines.
How they were made
GeneCAD with the hybrid decoder (
predict.sh --decoder hybrid, GeneCAD 0.6.0): a plain 5-state Viterbi decoding of the whole genome, then a local frame-aware step that completes partial genes and merges neighbouring genes on the same strand that belong together.ORF repair and ReelProtein refinement were run on the result. The files here are the final GFFs.
Every sequence of each genome was predicted. For the NAM lines, the sequences after the 50 longest were predicted later with GeneCAD commit fcc5c38 and added to the same files.
Pvulgaris (Phytozome v2.0 assembly,
Pvulgaris_442_v2.0) was added on 2026-10-19, predicted with GeneCAD commit fcc5c38 and the same model; all 27,069 transcripts were re-checked as complete ORFs.Every transcript has a complete ORF: ATG start, a single stop codon at the end and no unknown bases in the CDS. This is the check GeneCAD applies to rescued and merged genes since commit cae18bc. Genes from earlier runs that failed it were removed, and a merged gene that failed it was replaced by the genes it was made from when those have a complete ORF.
Vvinifera and Macuminata were updated on 2026-10-20 from whole-genome development runs using GeneCAD commit
fcc5c38and the existing deployed eight-species checkpointplantcad/genecad_plant@9fb642bb. They are not predictions from the revised MMLR-filtered training experiments. Earlier files remain in dataset history. Counts, output checksums and run provenance are in the update manifest.Tripsicum PanAnd reference haplotype annotations were added starting on 2026-10-21, using GeneCAD 0.6.1 (source commit
565be30plus the recorded source snapshot), the deployed plant model and hybrid decoding of all input sequences. Input/output checksums, model revisions and feature counts are in Tripsicum run provenance.Five benchmark genomes were added on 2026-10-26 with the same deployed checkpoint
plantcad/genecad_plant@9fb642bband hybrid decoding: Ccar (Cynara cardunculus), Egui (Elaeis guineensis), Jregia (Juglans regia), Ntabacum (Nicotiana tabacum) and Twil (Tripterygium wilfordii). GeneCAD source commit565be30; for Jregia, Egui and Ntabacum the merge step reads its input list from a file, which avoids the argument-length limit on assemblies with many sequences (inference unchanged). Every transcript was re-checked as a complete ORF. They are not predictions from the revised MMLR-filtered training experiments. Assemblies, checksums and run provenance are in the update manifest.Nsylvestris (Nicotiana sylvestris, RefSeq GCF_000393655.2) was added on 2026-10-27 with the same deployed checkpoint
plantcad/genecad_plant@9fb642bb, hybrid decoding and source as the 2026-10-26 Ntabacum run (565be30with the file-based merge input). Every transcript was re-checked as a complete ORF. Checksum and run provenance are in the update manifest.Graimondii (Gossypium raimondii, CNCB Genome Warehouse GWHBISS00000000) was added on 2026-10-29 with the deployed checkpoint
plantcad/genecad_plant@9fb642bb, hybrid decoding and the same source as the 2026-10-27 Nsylvestris run. Sequence names are the first field of the GWH FASTA headers (GWHBISS00000001-13). Every transcript was re-checked as a complete ORF. Checksums and run provenance are in the update manifest.Garboreum (Gossypium arboreum cv. Shixiya1, assembly WHUv3.0rc) was added on 2026-10-29 with the deployed checkpoint
plantcad/genecad_plant@9fb642bb, hybrid decoding and the same source as Graimondii. Every transcript was re-checked as a complete ORF. Checksums and run provenance are in the update manifest.Slycopersicum (Solanum lycopersicum Heinz 1706, assembly SL5.0, Phytozome V13 / ITAG5.0) was added on 2026-10-30 with the deployed checkpoint
plantcad/genecad_plant@9fb642bb, hybrid decoding and the same source as Garboreum. Every transcript was re-checked as a complete ORF. Checksums and run provenance are in the update manifest.
Layout
species/<species>/<species>_GeneCAD_final.gff
NAM/<line>/<line>_GeneCAD_final.gff
GFF notes
- Genes are numbered per sequence, for example
Chr1_gene_12. Transcripts carryorf_status. hybrid=rescued: a partial gene that the frame-aware step completed.hybrid=merged;merged_from=A,B: genes A and B were joined into one.- No partial genes are left in these files.
Assemblies
The genome assembly each GFF was predicted on. Input FASTA is the file given to GeneCAD and
SHA-256 is the checksum of that file, so an assembly can be matched exactly even if its name is ambiguous.
The 65 PlantCAD2 genomes used the soft-masked FASTA files of the PlantCAD2 genome set; the assembly column
gives the Phytozome genome entry from the PlantCAD2 genome list. The same table is in
provenance/assemblies.tsv.
| Set | Name | Organism | Assembly | Source | Input FASTA | SHA-256 |
|---|---|---|---|---|---|---|
| species | Acoerulea | Aquilegia coerulea | Aquilegia coerulea v3.1 | Phytozome, PlantCAD2 genome set | Acoerulea.softmasked_all.fa.gz |
b1481157dcd6c866e018115095414e062ae5339cab992fae1c02775d7c92aff4 |
| species | Acomosus | Ananas comosus | Ananas comosus v3 | Phytozome, PlantCAD2 genome set | Acomosus.softmasked_all.fa.gz |
0ea656e686e50d1cb8d597f57d785ad79c538660fe9ddb1db2fba2ea408fe823 |
| species | Ahypochondriacus | Amaranthus hypochondriacus | Amaranthus hypochondriacus v2.1 | Phytozome, PlantCAD2 genome set | Ahypochondriacus.softmasked_all.fa.gz |
6322a4ba847f22753619e09931a758ea16c98806898a0c1b20401200c42368d2 |
| species | Ahypogaea | Arachis hypogaea | Arachis hypogaeaLine8 v1.3 | Phytozome, PlantCAD2 genome set | Ahypogaea.softmasked_all.fa.gz |
bc08d535a35d3f3619068f6051306acd36f39ccd091c1722344ea439d1b60274 |
| species | Aofficinalis | Asparagus officinalis | Asparagus officinalis V1.1 | Phytozome, PlantCAD2 genome set | Aofficinalis.softmasked_all.fa.gz |
a147b1d09868973e7de727412afeaa62d874ed3a5abc23bda20e62ac452d0150 |
| species | Athaliana | Arabidopsis thaliana | Arabidopsis thaliana Araport11 | Phytozome, PlantCAD2 genome set | Athaliana.softmasked_all.fa.gz |
c9e328276572eb9cb9fdc3c67513112e676722561a63de014fefaaf77f391877 |
| species | Bdistachyon | Brachypodium distachyon | version not recorded (first sequence Bd1 75,071,545 bp) | Phytozome, PlantCAD2 genome set | Bdistachyon.softmasked_all.fa.gz |
52229d9a56783a21a5d9a3dc9233a4698fabf8778aa6d0f42abc9050b8b24ff7 |
| species | Bplatyphylla | Betula platyphylla | Betula platyphylla v1.1 | Phytozome, PlantCAD2 genome set | Bplatyphylla.softmasked_all.fa.gz |
8f4558df11db641527f823617f43171db4731eb5e1bcbadfffff9ab4c3d292e0 |
| species | Bstricta | Boechera stricta | Boechera stricta v1.2 | Phytozome, PlantCAD2 genome set | Bstricta.softmasked_all.fa.gz |
21911cfcf296d620d88494664c24845fc6d03430f4f31ac280e585a4c0a16cc0 |
| species | Bvulgaris | Beta vulgaris | Beta vulgaris ssp. vulgaris EL10.2_2 | Phytozome, PlantCAD2 genome set | Bvulgaris.softmasked_all.fa.gz |
2decab59980b72624a6a9c4da0a519e81f9f254e7783aa95f41ac7844cb8bbe2 |
| species | Carabica | Coffea arabica | Coffea arabica geisha 1.0 | Phytozome, PlantCAD2 genome set | Carabica.softmasked_all.fa.gz |
a84f255345c167a0d6f6fd366d00fe1949c9a9c637d45907a1957fc11e3333d3 |
| species | Carietinum | Cicer arietinum | Cicer arietinum v1.0 | Phytozome, PlantCAD2 genome set | Carietinum.softmasked_all.fa.gz |
7cf0546dd3f91406cbce0936403e5e210543df702df516180d40606eecd23d33 |
| species | Cavellana | Corylus avellana | Corylus avellana cv. Jefferson HAP1 v4.0 | Phytozome, PlantCAD2 genome set | Cavellana.softmasked_all.fa.gz |
02ade501fa347ef398de2a011dfc6694900ac60559435f1ebaee59f398906dd6 |
| species | Ccar | Cynara cardunculus | CcrdV1.1 (GCF_001531365.2) | NCBI RefSeq | GCF_001531365.2_CcrdV1.1_genomic.fna |
5551732827e569f530b1c99c10ba1859530fbfcd5cf8ec46f05261a55257d302 |
| species | Ccitriodora | Corymbia citriodora | Corymbia citriodora v2.1 | Phytozome, PlantCAD2 genome set | Ccitriodora.softmasked_all.fa.gz |
127c39b2d0ce7c578aa9f23e9033514de1c82d99b3cbea922df7cc325cd6162e |
| species | Cclementina | Citrus clementina | Citrus clementina v1.0 | Phytozome, PlantCAD2 genome set | Cclementina.softmasked_all.fa.gz |
248eebeeff36e3087e073ab22c98224467a2cb4f403ec1e9595f99e4d55a1645 |
| species | Cillinoinensis | Carya illinoinensis | Carya illinoinensis Pawnee v1.1 | Phytozome, PlantCAD2 genome set | Cillinoinensis.softmasked_all.fa.gz |
1a2ecd8eb17533c00b3c1b7f8409085208db0e8f79b930daa18e8a410cf33ff9 |
| species | Ckanehirae | Cinnamomum kanehirae | Cinnamomum kanehirae v3 | Phytozome, PlantCAD2 genome set | Ckanehirae.softmasked_all.fa.gz |
3e71c763ec852600ab32aeeb85efbe11d75f166271dfafc1742d5e229641a7b5 |
| species | Cquinoa | Chenopodium quinoa | Chenopodium quinoa v1.0 | Phytozome, PlantCAD2 genome set | Cquinoa.softmasked_all.fa.gz |
dae6fc04cf8594cd293e563d32cf57d1495f15bb42ca817bc08c5366f391b9bf |
| species | Crubella | Capsella rubella | Capsella rubella v1.1 | Phytozome, PlantCAD2 genome set | Crubella.softmasked_all.fa.gz |
cde6f32924a270bf9f6c47a1e2e5e0aeb51b7b344359f6f4a8c13bb195b2acf8 |
| species | Csativus | Cucumis sativus | Cucumis sativus v1.0 | Phytozome, PlantCAD2 genome set | Csativus.softmasked_all.fa.gz |
1bcf2e02d7067dcd5277266907c227b2f6cdb7b3c13f389175cfd1ef13889bc1 |
| species | Dalata | Dioscorea alata | Dioscorea alata v2.1 | Phytozome, PlantCAD2 genome set | Dalata.softmasked_all.fa.gz |
edfb43a5fa22b644be83cec89e9fbfef3660cede268d6cfbe8b68b9c93a44587 |
| species | Dcarota | Daucus carota | Daucus carota subsp. sativus v3.0 | Phytozome, PlantCAD2 genome set | Dcarota.softmasked_all.fa.gz |
a572ce6499d7aa958c62879457c1f5360739ca0833cc0c52a1d15aeb7a5b7f2b |
| species | Ecoracana | Eleusine coracana | Eleusine coracana v1.1 | Phytozome, PlantCAD2 genome set | Ecoracana.softmasked_all.fa.gz |
d19feca8ef6aa71d34ad621c29e6a6ef4fb877bbad615f916892df9944ff843f |
| species | Egrandis | Eucalyptus grandis | Eucalyptus grandis v2.0 | Phytozome, PlantCAD2 genome set | Egrandis.softmasked_all.fa.gz |
7579411d0e58b77af80590b96239497db5824dfe17d1ff5e10bb96c569ee42fb |
| species | Egui | Elaeis guineensis | EG11 (GCF_000442705.2) | NCBI RefSeq | GCF_000442705.2_EG11_genomic.fna |
0ecae861154b52c6439e737fe9bcf1ed65995d6291dfe7390c5c286f1e76dd2b |
| species | Esalsugineum | Eutrema salsugineum | Eutrema salsugineum v1.0 | Phytozome, PlantCAD2 genome set | Esalsugineum.softmasked_all.fa.gz |
8893ff4ee741da022fe019f687a15a58a25ad0b988926c5dbebd93822a8ad05e |
| species | Fvesca | Fragaria vesca | Fragaria vesca v4.0.a2 | Phytozome, PlantCAD2 genome set | Fvesca.softmasked_all.fa.gz |
c98c07c2b3e55142ec7120ff6de7b7a0c750644dabe19c8c5e9e60d272803c26 |
| species | Garboreum | Gossypium arboreum | cv. Shixiya1 WHUv3.0rc | Wuhan University (Shixiya1 v3.0rc) | Garboreum_Shixiya1_WHUv3.0rc.genome.standard.fa.gz; headers cut to the first field |
1bdbe64733c44d611714b2b3b5f44d54b1c21dbd38d804cffe13449a09b6dc1a |
| species | Gmax | Glycine max | Glycine max Wm82.a6.v1 | Phytozome, PlantCAD2 genome set | Gmax.softmasked_all.fa.gz |
6d4c75a0ae80ab0df2013e61c95584088ef30e815920e5b4130d9dca3ff33445 |
| species | Graimondii | Gossypium raimondii | GWHBISS00000000 | CNCB Genome Warehouse | GWHBISS00000000.genome.fasta.gz; headers cut to the first field |
8decb7ce878cccb0fa31181b809a53dabcd050647e253688debccd2a2ca3b010 |
| species | Hannuus | Helianthus annuus | Helianthus annuus r1.2 | Phytozome, PlantCAD2 genome set | Hannuus.softmasked_all.fa.gz |
a6085c46b93bf9a59a50b98baf22c488aa9a947c28bfbd241d2c56a62ec116c4 |
| species | Hvulgare | Hordeum vulgare | Hordeum vulgare Morex V3 | Phytozome, PlantCAD2 genome set | Hvulgare.softmasked_all.fa.gz |
bcda4499b235055333c5889812343042378e7ca2f6793d7423c8b934d4922f48 |
| species | Jregia | Juglans regia | Walnut_2.0, toplevel | Ensembl Plants release 60 | Juglans_regia.Walnut_2.0.dna.toplevel.fa |
85c9cd8304b1c7aa2ec892cea084b3c9474d8c34197ddcdd204d3033adfad272 |
| species | Lalbus | Lupinus albus | Lupinus albus v1 | Phytozome, PlantCAD2 genome set | Lalbus.softmasked_all.fa.gz |
9136303dc043d0f2268e5858ea42349411fe786b3fe1331755047258584ffbc8 |
| species | Lervoides | Lens ervoides | Lens ervoides v1 | Phytozome, PlantCAD2 genome set | Lervoides.softmasked_all.fa.gz |
c0fa757e1ac2fb97fc0202b55b9d98be56ebe740287150bbefd27c105e4eb55a |
| species | Ljaponicus | Lotus japonicus | Lotus japonicus Lj1.0v1 | Phytozome, PlantCAD2 genome set | Ljaponicus.softmasked_all.fa.gz |
b9653af6c1b81d704c89d8e22f76f0aa1aee8753ab7c94ec2313ba0724033d58 |
| species | Lsativa | Lactuca sativa | Lactuca sativa V8 | Phytozome, PlantCAD2 genome set | Lsativa.softmasked_all.fa.gz |
28d5ba6d6ff4802cd685cbf5a27360bfcbe734c351487fc85f58449cb727b4c3 |
| species | Lusitatissimum | Linum usitatissimum | Linum usitatissimum v1.0 | Phytozome, PlantCAD2 genome set | Lusitatissimum.softmasked_all.fa.gz |
660f4a9cda92da85130703ca0aa697045dbcbb24294dd76999ebb1233c5706c0 |
| species | Macuminata | Musa acuminata | Musa acuminata v1 | Phytozome, PlantCAD2 genome set | Macuminata.softmasked_all.fa.gz (run-host copy) |
3335a30234a56b9029b459c34957868e6a4834cbcb0db8db452430e71afc728f |
| species | Mdomestica | Malus domestica | Malus domestica v1.1 | Phytozome, PlantCAD2 genome set | Mdomestica.softmasked_all.fa.gz |
981c365c400c2d4444d4ce7198612c704bc8c521c1eb17732b0f0a96726be99f |
| species | Mesculenta | Manihot esculenta | Manihot esculenta v8.1 | Phytozome, PlantCAD2 genome set | Mesculenta.softmasked_all.fa.gz |
e34e58586dabf28bffda87b2337bf46a3410158ee37bdddc9dd400f5a7b1a4a8 |
| species | Msinensis | Miscanthus sinensis | Miscanthus sinensis v7.1 | Phytozome, PlantCAD2 genome set | Msinensis.softmasked_all.fa.gz |
e3e0de4a84072dcefcd6a2732f939e57101bbecf0331a71a3c102bb8c9f7cac1 |
| species | Mtruncatula | Medicago truncatula | Medicago truncatula Mt4.0v1 | Phytozome, PlantCAD2 genome set | Mtruncatula.softmasked_all.fa.gz |
13f809156c255da975b22feddbed7bf5211d3abeaa661176b9213b0d51ecef08 |
| species | Ncolorata | Nymphaea colorata | Nymphaea colorata v1.2 | Phytozome, PlantCAD2 genome set | Ncolorata.softmasked_all.fa.gz |
783bf27c81ac94eaa9edd68edd0bf7154b314e8852e3c897ee74e38c9cfe6d9e |
| species | Nsylvestris | Nicotiana sylvestris | ASM39365v2 (GCF_000393655.2) | NCBI RefSeq | GCF_000393655.2_ASM39365v2_genomic.fna |
7caef8c197491d9b957d5b8b830fdd45d075e2aec747d14ea29512da93dab27d |
| species | Ntabacum | Nicotiana tabacum | ASM71507v2 (GCF_000715075.1) | NCBI RefSeq | GCF_000715075.1_ASM71507v2_genomic.fna |
37c5f146cbad02cffa28fb4c56cdd8683c6bd8734dab9106ffae746fc2b2d4c2 |
| species | Oeuropaea | Olea europaea | Olea europaea v1.0 | Phytozome, PlantCAD2 genome set | Oeuropaea.softmasked_all.fa.gz |
aba9bb8629668f003a25ceb13f94ce0fd2d2da1f76cc8bd7ad41840d1a8c6511 |
| species | Osativa | Oryza sativa | Oryza sativa v7.0 | Phytozome, PlantCAD2 genome set | Osativa.softmasked_all.fa.gz |
9bfe2a13ddda3822b8fa3f6d457b1e90cd4c659f1a83919c9224fe208b570830 |
| species | Othomaeum | Oropetium thomaeum | Oropetium thomaeum v1.0 | Phytozome, PlantCAD2 genome set | Othomaeum.softmasked_all.fa.gz |
8576020fa55ecfd01125c39c970109cd14a9110b3b2ada54678d6c3f298c91b1 |
| species | Pamilis | Portulaca amilis | Portulaca amilis v1.0 | Phytozome, PlantCAD2 genome set | Pamilis.softmasked_all.fa.gz |
b1e7047fb888afb4af886362042f1028c0f74e2cb561b805b14caba41c992fc0 |
| species | Ppersica | Prunus persica | Prunus persica v2.1 | Phytozome, PlantCAD2 genome set | Ppersica.softmasked_all.fa.gz |
4dfb61b1678ff038f0cf4f1e12c12d1337cb86bad15df0e13c044f02da981337 |
| species | Ptrichocarpa | Populus trichocarpa | Populus trichocarpa v4.1 | Phytozome, PlantCAD2 genome set | Ptrichocarpa.softmasked_all.fa.gz |
962fe509334c466eca1edc43fa5d9535ca2cd251dc859d0fd1a49768d031975b |
| species | Ptrifoliata | Poncirus trifoliata | Poncirus trifoliata v1.3.1 | Phytozome, PlantCAD2 genome set | Ptrifoliata.softmasked_all.fa.gz |
476ea4e901761de2e94802ad92f24cd45dcdeb7ff14da734c7c8c581ea2765f7 |
| species | Pvaginatum | Paspalum vaginatum | Paspalum vaginatum v3.1 | Phytozome, PlantCAD2 genome set | Pvaginatum.softmasked_all.fa.gz |
fb7cd853ab3f55cd0069dbcd0dd35819af7c32489179d51a79cb2ecb8c421c61 |
| species | Pvirgatum | Panicum virgatum | Panicum virgatum v5.1 | Phytozome, PlantCAD2 genome set | Pvirgatum.softmasked_all.fa.gz |
c61f8d9dd8132c2574ac940f21658d33bdcbafcf1d8a4fd8388ff5b9373e322b |
| species | Pvulgaris | Phaseolus vulgaris | Pvulgaris_442_v2.0 | Phytozome V12 | Pvulgaris_442_v2.0.fa.gz |
152e41c3168b0c7ca34d446e3d011178dd06999f6f6cf0db4b6cadf2bd401fda |
| species | Qrubra | Quercus rubra | Quercus rubra v2.1 | Phytozome, PlantCAD2 genome set | Qrubra.softmasked_all.fa.gz |
b82e59e47c6a2222f93f407cf70cf30f0f83fdc41c8323c6787b805c15a23704 |
| species | Rcommunis | Ricinus communis | Ricinus communis v0.1 | Phytozome, PlantCAD2 genome set | Rcommunis.softmasked_all.fa.gz |
d9d8367181fd9bb21a5d4329ab5efb6615c7611fe6b3e2db475aded764bd230b |
| species | Sbicolor | Sorghum bicolor | version not recorded (first sequence Chr01 80,884,392 bp) | Phytozome, PlantCAD2 genome set | Sbicolor.softmasked_all.fa |
5b3b27edefa0fdcbdfdbad4f3557788bcd817490a0196e4269a93bbe2e94f836 |
| species | Slycopersicum | Solanum lycopersicum | Slycopersicum_796_SL5.0 (Heinz 1706, SL5.0; ITAG5.0) | Phytozome V13 | Slycopersicum_796_SL5.0.fa.gz |
cbfe0616b5bf9b48a0f33dd1ce76144de6d5dd3d252e614174a0038ff7da2469 |
| species | Soleracea | Spinacia oleracea | Spinacia oleracea Spov3 | Phytozome, PlantCAD2 genome set | Soleracea.softmasked_all.fa.gz |
4bb04878853bf6a6dd1016b5554b6bf77ad5a2ccd9b813b1875bb807a4a82891 |
| species | Sparvula | Schrenkiella parvula | Schrenkiella parvula v2.2 | Phytozome, PlantCAD2 genome set | Sparvula.softmasked_all.fa |
3ee1617a2e3d2d27c694f0e32e27829f76e7251fa03abf148cc2425f48394b17 |
| species | Spolyrhiza | Spirodela polyrhiza | Spirodela polyrhiza v2 | Phytozome, PlantCAD2 genome set | Spolyrhiza.softmasked_all.fa.gz |
0cfbb4ecc239378030b874f1bed68af3e3a15ccb96250f91ff8da5704fb7ce71 |
| species | Spurpurea | Salix purpurea | Salix purpurea v5.1 | Phytozome, PlantCAD2 genome set | Spurpurea.softmasked_all.fa.gz |
a08fa67ab209e7baa57eddad27df4a99f93085405eb9e06db52b41bd30786d98 |
| species | Sviridis | Setaria viridis | version not recorded (first sequence Chr_01 41,732,233 bp) | Phytozome, PlantCAD2 genome set | Sviridis.softmasked_all.fa.gz |
8c4808e27fa0426031648666295bc8a48a05c472dadfadfe513330ee2195dae8 |
| species | Taestivum | Triticum aestivum | Triticum aestivum cv. Chinese Spring v2.1 | Phytozome, PlantCAD2 genome set | Taestivum.softmasked_all.fa.gz |
5998a49d512028a59cee6218fd764ec0609616e058b571e3d189219c11b180a7 |
| species | Td-FL_9056069_6-REFERENCE-PanAnd-2.0a | Tripsacum dactyloides | Td-FL_9056069_6-REFERENCE-PanAnd-2.0a | PanAnd 2.0 reference haplotype | Td-FL_9056069_6-REFERENCE-PanAnd-2.0a.fasta.gz |
a5f845c85126a5f9b5b631bc57d87d24e863a100a57ac0d5783e002de6577e17 |
| species | Td-FL_9056069_6-REFERENCE-PanAnd-2.0b | Tripsacum dactyloides | Td-FL_9056069_6-REFERENCE-PanAnd-2.0b | PanAnd 2.0 reference haplotype | Td-FL_9056069_6-REFERENCE-PanAnd-2.0b.fasta.gz |
41a1851e2b6dc7fa88d3f1bd4b3ae6d383c0ecd0a05f391ee10683d40d8621a1 |
| species | Td-KS_B6_1-REFERENCE-PanAnd-2.0a | Tripsacum dactyloides | Td-KS_B6_1-REFERENCE-PanAnd-2.0a | PanAnd 2.0 reference haplotype | Td-KS_B6_1-REFERENCE-PanAnd-2.0a.fasta.gz |
fd821e5a2f8eb8b8ad000e3a97d807c599dabef345f497b0f9477994004abdb2 |
| species | Td-KS_B6_1-REFERENCE-PanAnd-2.0b | Tripsacum dactyloides | Td-KS_B6_1-REFERENCE-PanAnd-2.0b | PanAnd 2.0 reference haplotype | Td-KS_B6_1-REFERENCE-PanAnd-2.0b.fasta.gz |
8a1f0e2d08db848bb46e08f8526e5572de9ac6745b1e8bbebfa7225ce898f2da |
| species | Tintermedium | Thinopyrum intermedium | Thinopyrum intermedium v3.1 | Phytozome, PlantCAD2 genome set | Tintermedium.softmasked_all.fa.gz |
6fd1404240bac85f134084d1f3d9db529a4486887814800e6f928dbd74e3bb48 |
| species | Twil | Tripterygium wilfordii | ASM1340144v1 (GCF_013401445.1) | NCBI RefSeq | GCF_013401445.1_ASM1340144v1_genomic.fna |
a94c6d70791f340e2fd2d96002b387832c709f00a1414dc59f16565bd2d0c193 |
| species | Vdarrowii | Vaccinium darrowii | Vaccinium darrowii v1.2 | Phytozome, PlantCAD2 genome set | Vdarrowii.softmasked_all.fa.gz |
9d4fd55bb953a50364ff1eb1ab457015bce41309769abc31c6c70191f977ddc2 |
| species | Vfaba | Vicia faba | Vicia faba v1.1 | Phytozome, PlantCAD2 genome set | Vfaba.softmasked_all.fa.gz |
f7536882f54685917c51e50c46f459857d74b0af6349d3f6fb2eed78cd17b322 |
| species | Vunguiculata | Vigna unguiculata | Vigna unguiculata v1.2 | Phytozome, PlantCAD2 genome set | Vunguiculata.softmasked_all.fa.gz |
e9e70299a58567b46eb2ea25fd96c6b147ce6357e9545de42100ab6fb7783ca3 |
| species | Vvinifera | Vitis vinifera | Vitis vinifera v2.1 | Phytozome, PlantCAD2 genome set | Vvinifera.softmasked_all.fa.gz (run-host copy) |
3b6d7fff9a2e40aedea9a751a0cc533df079feb9e5338331161c55b1404c2618 |
| species | Zmarina | Zostera marina | Zostera marina v3.1 | Phytozome, PlantCAD2 genome set | Zmarina.softmasked_all.fa.gz |
c7620f741810dd88eb7510d60b25bc45656fc75afa7781c32e4af6aaaf0e2b3c |
| species | Zmays | Zea mays | Zea mays Zm-B73-REFERENCE-NAM-5.0.55 | Phytozome, PlantCAD2 genome set | Zmays.softmasked_all.fa.gz |
5c0efff9d2bb1c026d0630e22cb3384ad9db5141a8dc0b3a2bfb570b018a474d |
| NAM | Zm-B73-REFERENCE-NAM-5.0 | Zea mays | Zm-B73-REFERENCE-NAM-5.0 | MaizeGDB (NAM founder assemblies) | Zm-B73-REFERENCE-NAM-5.0.fa.gz |
a40ee35888a9c0b956c448752f59637639a7906d7fa14971c9047eb088ded2c2 |
| NAM | Zm-B97-REFERENCE-NAM-1.0 | Zea mays | Zm-B97-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-B97-REFERENCE-NAM-1.0.fa.gz |
10c6f1358a88422cf894260c476b9e53d46cc9c5f62488e7f87226ba5faabf3c |
| NAM | Zm-CML103-REFERENCE-NAM-1.0 | Zea mays | Zm-CML103-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-CML103-REFERENCE-NAM-1.0.fa.gz |
fd0d6da20e4f77a9bb55acbe24b76ab22656f4434b454ab30018c0f364affe48 |
| NAM | Zm-CML228-REFERENCE-NAM-1.0 | Zea mays | Zm-CML228-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-CML228-REFERENCE-NAM-1.0.fa.gz |
071db2dea78d02ec7ff4e442e84763e7e54d446282c4578a230ba85db83f7241 |
| NAM | Zm-CML247-REFERENCE-NAM-1.0 | Zea mays | Zm-CML247-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-CML247-REFERENCE-NAM-1.0.fa.gz |
b7d8abc5f68927034bb34026eb8dee1c70267ec6e95b0eafd9579255b39d0531 |
| NAM | Zm-CML277-REFERENCE-NAM-1.0 | Zea mays | Zm-CML277-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-CML277-REFERENCE-NAM-1.0.fa.gz |
87024bd80e11e13c9fd1e34a8bd238184613e423eaaa800d7dd7ec4a6d0a16fd |
| NAM | Zm-CML322-REFERENCE-NAM-1.0 | Zea mays | Zm-CML322-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-CML322-REFERENCE-NAM-1.0.fa.gz |
875ef7617420317513d5c95b50832c913fe8ec94530c7d74a36075ba9b91cbb6 |
| NAM | Zm-CML333-REFERENCE-NAM-1.0 | Zea mays | Zm-CML333-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-CML333-REFERENCE-NAM-1.0.fa.gz |
f5b4c7e4bed29b62e115df7f7cfd5e80014b0e79ce4c342b53426eed2ab08760 |
| NAM | Zm-CML52-REFERENCE-NAM-1.0 | Zea mays | Zm-CML52-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-CML52-REFERENCE-NAM-1.0.fa.gz |
e6a18be0e42d2084e1a296db55b00ee97fafc332f7327f30cb24aab242800d96 |
| NAM | Zm-CML69-REFERENCE-NAM-1.0 | Zea mays | Zm-CML69-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-CML69-REFERENCE-NAM-1.0.fa.gz |
047305e399ee8ab2cff94e009056fbb46ffe1abcaf76be3ba208a45b8ed2bc9c |
| NAM | Zm-HP301-REFERENCE-NAM-1.0 | Zea mays | Zm-HP301-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-HP301-REFERENCE-NAM-1.0.fa.gz |
baeb81521fad1bffa16c9fc0225335de2acab66896cbb1698bbf8f64b42e3208 |
| NAM | Zm-Il14H-REFERENCE-NAM-1.0 | Zea mays | Zm-Il14H-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Il14H-REFERENCE-NAM-1.0.fa.gz |
289c74df9c993ee0dfc75be17604f35f4a45a9c164db4cb64edbf3a81cc32ed0 |
| NAM | Zm-Ki11-REFERENCE-NAM-1.0 | Zea mays | Zm-Ki11-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Ki11-REFERENCE-NAM-1.0.fa.gz |
51bc519c67803c21004b635f7300df4a644ccfe13ec7b2fa0ee1c393b75339b8 |
| NAM | Zm-Ki3-REFERENCE-NAM-1.0 | Zea mays | Zm-Ki3-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Ki3-REFERENCE-NAM-1.0.fa.gz |
a5593416ae7e80ad97505947ba880b29847f1f590988622d63540701a4a6568c |
| NAM | Zm-Ky21-REFERENCE-NAM-1.0 | Zea mays | Zm-Ky21-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Ky21-REFERENCE-NAM-1.0.fa.gz |
d94e7c18b1010a37fcd6c0a52c072e8636b704394efd95be6c3e7aa4a68b07ca |
| NAM | Zm-M162W-REFERENCE-NAM-1.0 | Zea mays | Zm-M162W-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-M162W-REFERENCE-NAM-1.0.fa.gz |
27ee86f2bf8e08c4b69a6e4ba65169b9c8d869994f63419f7641955417bc4656 |
| NAM | Zm-M37W-REFERENCE-NAM-1.0 | Zea mays | Zm-M37W-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-M37W-REFERENCE-NAM-1.0.fa.gz |
19168ea7be11cee1dbccd7a8202d9d55c64abf97ce1f4717c214beb0089105c8 |
| NAM | Zm-Mo18W-REFERENCE-NAM-1.0 | Zea mays | Zm-Mo18W-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Mo18W-REFERENCE-NAM-1.0.fa.gz |
dd66ad969b39db58624cfb12ad0490e6b21e960c479de427a18232acf36d65eb |
| NAM | Zm-Ms71-REFERENCE-NAM-1.0 | Zea mays | Zm-Ms71-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Ms71-REFERENCE-NAM-1.0.fa.gz |
17dfc51f4654be683454523778b12bb94c40ffa4ed633cf6e317df299d3c3d5f |
| NAM | Zm-NC350-REFERENCE-NAM-1.0 | Zea mays | Zm-NC350-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-NC350-REFERENCE-NAM-1.0.fa.gz |
4295a448572fa5f31018d0e6eaeef91f53bebfc7b370bd78e0d5876e3c27aa62 |
| NAM | Zm-NC358-REFERENCE-NAM-1.0 | Zea mays | Zm-NC358-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-NC358-REFERENCE-NAM-1.0.fa.gz |
67a3401d5aed6216676b5296df3b643d7e9f63d87226f50f618991b935b4dd19 |
| NAM | Zm-Oh43-REFERENCE-NAM-1.0 | Zea mays | Zm-Oh43-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Oh43-REFERENCE-NAM-1.0.fa.gz |
eea0375a3462b636c374e4ca3025f9399c23554c24303b4eca71a776ce14393d |
| NAM | Zm-Oh7B-REFERENCE-NAM-1.0 | Zea mays | Zm-Oh7B-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Oh7B-REFERENCE-NAM-1.0.fa.gz |
fc4811b23e92f2e696c511d999916d076e569b251b71c11e62120b295b358b56 |
| NAM | Zm-P39-REFERENCE-NAM-1.0 | Zea mays | Zm-P39-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-P39-REFERENCE-NAM-1.0.fa.gz |
c2ad98cf8283458529a6de2974ad3997d629a45b565ea0a39959c5a57359c282 |
| NAM | Zm-Tx303-REFERENCE-NAM-1.0 | Zea mays | Zm-Tx303-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Tx303-REFERENCE-NAM-1.0.fa.gz |
40e64ed013f68790e17bd5294febfcb61be173ebbc8bfef572ad45a260f9decd |
| NAM | Zm-Tzi8-REFERENCE-NAM-1.0 | Zea mays | Zm-Tzi8-REFERENCE-NAM-1.0 | MaizeGDB (NAM founder assemblies) | Zm-Tzi8-REFERENCE-NAM-1.0.fa.gz |
40b2294e9d30a466a07b68d68faac94336641acd21c37352aaefa4a0e10e1971 |
Contents
| Set | Name | Genes | Merged | Rescued |
|---|---|---|---|---|
| species | Acoerulea | 26,837 | 369 | 2,869 |
| species | Acomosus | 23,167 | 448 | 2,066 |
| species | Ahypochondriacus | 25,447 | 582 | 5,670 |
| species | Ahypogaea | 69,435 | 1,191 | 8,899 |
| species | Aofficinalis | 26,415 | 1,575 | 5,025 |
| species | Athaliana | 25,965 | 76 | 1,351 |
| species | Bdistachyon | 26,985 | 226 | 1,709 |
| species | Bplatyphylla | 32,115 | 629 | 5,309 |
| species | Bstricta | 25,824 | 339 | 2,499 |
| species | Bvulgaris | 22,599 | 546 | 1,725 |
| species | Carabica | 49,536 | 546 | 6,476 |
| species | Carietinum | 25,471 | 267 | 2,426 |
| species | Cavellana | 27,561 | 409 | 2,355 |
| species | Ccar | 25,260 | 285 | 1,363 |
| species | Ccitriodora | 38,975 | 588 | 5,161 |
| species | Cclementina | 25,063 | 287 | 2,627 |
| species | Cillinoinensis | 32,800 | 490 | 2,957 |
| species | Ckanehirae | 32,739 | 1,110 | 3,831 |
| species | Cquinoa | 47,577 | 1,055 | 5,638 |
| species | Crubella | 26,818 | 87 | 1,357 |
| species | Csativus | 20,184 | 203 | 955 |
| species | Dalata | 25,815 | 382 | 2,419 |
| species | Dcarota | 35,009 | 392 | 2,277 |
| species | Ecoracana | 60,399 | 643 | 5,571 |
| species | Egrandis | 42,423 | 1,060 | 7,127 |
| species | Egui | 33,442 | 670 | 4,205 |
| species | Esalsugineum | 25,843 | 163 | 1,964 |
| species | Fvesca | 27,073 | 233 | 2,581 |
| species | Gmax | 51,708 | 596 | 4,452 |
| species | Hannuus | 45,356 | 933 | 4,027 |
| species | Hvulgare | 38,780 | 737 | 3,242 |
| species | Jregia | 32,301 | 239 | 2,417 |
| species | Lalbus | 32,498 | 114 | 1,278 |
| species | Lervoides | 32,573 | 594 | 4,056 |
| species | Ljaponicus | 32,836 | 429 | 2,911 |
| species | Lsativa | 33,584 | 497 | 3,449 |
| species | Lusitatissimum | 41,488 | 440 | 5,393 |
| species | Macuminata | 33,091 | 289 | 2,114 |
| species | Mdomestica | 41,194 | 665 | 4,466 |
| species | Mesculenta | 31,051 | 307 | 1,857 |
| species | Msinensis | 63,022 | 1,968 | 10,108 |
| species | Mtruncatula | 34,364 | 330 | 2,765 |
| species | Ncolorata | 23,010 | 295 | 1,927 |
| species | Ntabacum | 57,843 | 631 | 4,474 |
| species | Nsylvestris | 29,812 | 346 | 2,068 |
| species | Garboreum | 35,797 | 282 | 3,389 |
| species | Graimondii | 36,327 | 251 | 3,049 |
| species | Slycopersicum | 27,300 | 182 | 1,448 |
| species | Oeuropaea | 38,231 | 1,164 | 4,736 |
| species | Osativa | 31,877 | 398 | 2,687 |
| species | Othomaeum | 25,970 | 207 | 1,972 |
| species | Pamilis | 27,638 | 399 | 2,446 |
| species | Ppersica | 24,729 | 182 | 1,695 |
| species | Ptrichocarpa | 33,594 | 223 | 2,038 |
| species | Ptrifoliata | 24,103 | 193 | 2,014 |
| species | Pvaginatum | 31,959 | 431 | 2,854 |
| species | Pvirgatum | 64,417 | 1,153 | 7,821 |
| species | Pvulgaris | 27,069 | 118 | 1,392 |
| species | Qrubra | 37,650 | 793 | 5,018 |
| species | Rcommunis | 21,410 | 153 | 2,467 |
| species | Sbicolor | 29,944 | 305 | 1,890 |
| species | Soleracea | 26,899 | 679 | 3,172 |
| species | Sparvula | 23,735 | 66 | 1,730 |
| species | Spolyrhiza | 16,577 | 206 | 2,144 |
| species | Spurpurea | 33,969 | 343 | 3,441 |
| species | Sviridis | 31,222 | 263 | 2,199 |
| species | Taestivum | 164,601 | 3,187 | 18,826 |
| species | Td-FL_9056069_6-REFERENCE-PanAnd-2.0a | 40,592 | 691 | 3,990 |
| species | Td-FL_9056069_6-REFERENCE-PanAnd-2.0b | 40,540 | 759 | 4,043 |
| species | Td-KS_B6_1-REFERENCE-PanAnd-2.0a | 40,703 | 650 | 4,036 |
| species | Td-KS_B6_1-REFERENCE-PanAnd-2.0b | 39,616 | 620 | 3,731 |
| species | Tintermedium | 190,698 | 4,473 | 25,008 |
| species | Twil | 33,239 | 180 | 2,533 |
| species | Vdarrowii | 34,510 | 787 | 3,834 |
| species | Vfaba | 36,900 | 763 | 4,709 |
| species | Vunguiculata | 28,981 | 251 | 1,917 |
| species | Vvinifera | 27,975 | 357 | 2,794 |
| species | Zmarina | 19,649 | 253 | 1,797 |
| species | Zmays | 37,774 | 919 | 3,686 |
| NAM | Zm-B73-REFERENCE-NAM-5.0 | 37,887 | 918 | 3,715 |
| NAM | Zm-B97-REFERENCE-NAM-1.0 | 37,384 | 865 | 3,658 |
| NAM | Zm-CML103-REFERENCE-NAM-1.0 | 37,480 | 858 | 3,872 |
| NAM | Zm-CML228-REFERENCE-NAM-1.0 | 39,034 | 910 | 4,144 |
| NAM | Zm-CML247-REFERENCE-NAM-1.0 | 37,783 | 862 | 3,897 |
| NAM | Zm-CML277-REFERENCE-NAM-1.0 | 37,540 | 874 | 3,816 |
| NAM | Zm-CML322-REFERENCE-NAM-1.0 | 37,497 | 934 | 3,689 |
| NAM | Zm-CML333-REFERENCE-NAM-1.0 | 37,613 | 900 | 3,848 |
| NAM | Zm-CML52-REFERENCE-NAM-1.0 | 39,245 | 867 | 4,195 |
| NAM | Zm-CML69-REFERENCE-NAM-1.0 | 37,812 | 901 | 3,835 |
| NAM | Zm-HP301-REFERENCE-NAM-1.0 | 37,317 | 838 | 3,716 |
| NAM | Zm-Il14H-REFERENCE-NAM-1.0 | 37,205 | 855 | 3,629 |
| NAM | Zm-Ki11-REFERENCE-NAM-1.0 | 38,303 | 967 | 3,955 |
| NAM | Zm-Ki3-REFERENCE-NAM-1.0 | 37,548 | 891 | 3,839 |
| NAM | Zm-Ky21-REFERENCE-NAM-1.0 | 37,404 | 859 | 3,698 |
| NAM | Zm-M162W-REFERENCE-NAM-1.0 | 37,382 | 882 | 3,703 |
| NAM | Zm-M37W-REFERENCE-NAM-1.0 | 37,601 | 858 | 3,786 |
| NAM | Zm-Mo18W-REFERENCE-NAM-1.0 | 37,545 | 867 | 3,767 |
| NAM | Zm-Ms71-REFERENCE-NAM-1.0 | 38,017 | 911 | 3,805 |
| NAM | Zm-NC350-REFERENCE-NAM-1.0 | 38,198 | 899 | 4,045 |
| NAM | Zm-NC358-REFERENCE-NAM-1.0 | 37,770 | 942 | 3,800 |
| NAM | Zm-Oh43-REFERENCE-NAM-1.0 | 37,912 | 970 | 3,735 |
| NAM | Zm-Oh7B-REFERENCE-NAM-1.0 | 37,526 | 892 | 3,779 |
| NAM | Zm-P39-REFERENCE-NAM-1.0 | 37,657 | 878 | 3,783 |
| NAM | Zm-Tx303-REFERENCE-NAM-1.0 | 38,089 | 885 | 3,868 |
| NAM | Zm-Tzi8-REFERENCE-NAM-1.0 | 38,533 | 916 | 4,063 |
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