diff --git a/.gitattributes b/.gitattributes index bed0738c7eeb449bca98b5d2f33c89a1ee56349a..ee2e89d83dd9b33bd85761a70662bdedd495c5a3 100644 --- a/.gitattributes +++ b/.gitattributes @@ -58,3 +58,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text # Video files - compressed *.mp4 filter=lfs diff=lfs merge=lfs -text *.webm filter=lfs diff=lfs merge=lfs -text +GCF_003473485.1_MtrunA17r5.0-ANR/genome.fa.gz.gzi filter=lfs diff=lfs merge=lfs -text +GCF_016808095.1_ASM1680809v1/genome.fa.gz.gzi filter=lfs diff=lfs merge=lfs -text +GCF_030704535.1_ASM3070453v1/genome.fa.gz.gzi filter=lfs diff=lfs merge=lfs -text diff --git a/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz b/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz new file mode 100644 index 0000000000000000000000000000000000000000..94d9b7b6dc5334143a0d15cb53a4a4336974ab09 --- /dev/null +++ b/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:16f0f8f954abddb5acf3f2aab6beb26b6271ce423ba249d62a3285b1e308addd +size 129705072 diff --git a/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz.fai b/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz.fai new file mode 100644 index 0000000000000000000000000000000000000000..894e3e1510fb69f71633c526ee0218a5d54dbdb7 --- /dev/null +++ b/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz.fai @@ -0,0 +1,24 @@ +NC_037285.2 49788581 13 60 61 +NC_037286.2 25242375 50618417 60 61 +NC_037287.2 21678634 76281512 60 61 +NC_037288.2 24140038 98321470 60 61 +NC_037289.2 24981103 122863855 60 61 +NC_037290.2 27516652 148261323 60 61 +NC_037291.2 15561420 176236599 60 61 +NC_037292.2 19195260 192057389 60 61 +NC_037293.2 12987399 211572583 60 61 +NC_037294.2 22799081 224776452 60 61 +NC_037295.2 19288771 247955531 60 61 +NC_037296.2 15589050 267565795 60 61 +NC_037297.2 15705617 283414676 60 61 +NC_037298.2 17801709 299382067 60 61 +NC_037299.2 15231745 317480485 60 61 +NC_037300.2 14619816 332966106 60 61 +NC_037301.2 15189755 347829599 60 61 +NC_037302.2 16264003 363272530 60 61 +NC_037303.2 15623655 379807613 60 61 +NW_026291139.1 640640 395691679 60 61 +NW_026291140.1 362030 396343013 60 61 +NW_026291141.1 298400 396711093 60 61 +NW_026291142.1 239390 397014483 60 61 +NC_009143.1 157033 397257876 60 61 diff --git a/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz.gzi b/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz.gzi new file mode 100644 index 0000000000000000000000000000000000000000..8abcff7733d602d088e10bab6140dc3ea220c9a2 Binary files /dev/null and b/GCF_000002775.5_P.trichocarpa_v4.1/genome.fa.gz.gzi differ diff --git a/GCF_000002775.5_P.trichocarpa_v4.1/labels.bed.gz b/GCF_000002775.5_P.trichocarpa_v4.1/labels.bed.gz new file mode 100644 index 0000000000000000000000000000000000000000..bfb5f55a7478ddc568594ca957407def4d18e085 --- /dev/null +++ b/GCF_000002775.5_P.trichocarpa_v4.1/labels.bed.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a24494b181fa39ab416f808ec3228a66f80cee3c5f56fadaa1b7f17b8d1ad1f9 +size 4109122 diff --git a/GCF_000002775.5_P.trichocarpa_v4.1/prediction.gff3 b/GCF_000002775.5_P.trichocarpa_v4.1/prediction.gff3 new file mode 100644 index 0000000000000000000000000000000000000000..f79d719c0b18c2e0734782c1e99703e4bd362cae --- /dev/null +++ b/GCF_000002775.5_P.trichocarpa_v4.1/prediction.gff3 @@ -0,0 +1,38 @@ +##gff-version 3 +NC_009143.1 NTv3 gene 1 40960 . - . ID=gene_18_m +NC_009143.1 NTv3 intron 1 40960 . - . ID=gene_18_m_intron_1;Parent=gene_18_m +NC_009143.1 NTv3 gene 8193 32661 . + . ID=gene_1_p +NC_009143.1 NTv3 intron 8193 32654 . + . ID=gene_1_p_intron_8193;Parent=gene_1_p +NC_009143.1 NTv3 CDS 32655 32661 . + 1 ID=gene_1_p_CDS_32655;Parent=gene_1_p +NC_009143.1 NTv3 gene 32769 81833 . + . ID=gene_2_p +NC_009143.1 NTv3 intron 32769 81826 . + . ID=gene_2_p_intron_32769;Parent=gene_2_p +NC_009143.1 NTv3 gene 41054 49152 . - . ID=gene_19_m +NC_009143.1 NTv3 CDS 41054 41060 . - 1 ID=gene_19_m_CDS_41054;Parent=gene_19_m +NC_009143.1 NTv3 intron 41061 49152 . - . ID=gene_19_m_intron_41061;Parent=gene_19_m +NC_009143.1 NTv3 gene 49276 73728 . - . ID=gene_20_m +NC_009143.1 NTv3 CDS 49276 49282 . - 1 ID=gene_20_m_CDS_49276;Parent=gene_20_m +NC_009143.1 NTv3 intron 49283 73728 . - . ID=gene_20_m_intron_49283;Parent=gene_20_m +NC_009143.1 NTv3 gene 73846 81920 . - . ID=gene_21_m +NC_009143.1 NTv3 CDS 73846 73852 . - 1 ID=gene_21_m_CDS_73846;Parent=gene_21_m +NC_009143.1 NTv3 intron 73853 81920 . - . ID=gene_21_m_intron_73853;Parent=gene_21_m +NC_009143.1 NTv3 CDS 81827 81833 . + 1 ID=gene_2_p_CDS_81827;Parent=gene_2_p +NC_009143.1 NTv3 gene 81921 98189 . + . ID=gene_3_p +NC_009143.1 NTv3 intron 81921 98182 . + . ID=gene_3_p_intron_81921;Parent=gene_3_p +NC_009143.1 NTv3 gene 82015 122880 . - . ID=gene_22_m +NC_009143.1 NTv3 CDS 82015 82024 . - 1 ID=gene_22_m_CDS_82015;Parent=gene_22_m +NC_009143.1 NTv3 intron 82025 122880 . - . ID=gene_22_m_intron_82025;Parent=gene_22_m +NC_009143.1 NTv3 CDS 98183 98189 . + 1 ID=gene_3_p_CDS_98183;Parent=gene_3_p +NC_009143.1 NTv3 gene 98305 106386 . + . ID=gene_4_p +NC_009143.1 NTv3 intron 98305 106382 . + . ID=gene_4_p_intron_98305;Parent=gene_4_p +NC_009143.1 NTv3 CDS 106383 106386 . + 1 ID=gene_4_p_CDS_106383;Parent=gene_4_p +NC_009143.1 NTv3 gene 106497 130969 . + . ID=gene_5_p +NC_009143.1 NTv3 intron 106497 130965 . + . ID=gene_5_p_intron_106497;Parent=gene_5_p +NC_009143.1 NTv3 gene 123007 139264 . - . ID=gene_23_m +NC_009143.1 NTv3 CDS 123007 123010 . - 1 ID=gene_23_m_CDS_123007;Parent=gene_23_m +NC_009143.1 NTv3 intron 123011 139264 . - . ID=gene_23_m_intron_123011;Parent=gene_23_m +NC_009143.1 NTv3 CDS 130966 130969 . + 1 ID=gene_5_p_CDS_130966;Parent=gene_5_p +NC_009143.1 NTv3 gene 131073 157033 . + . ID=gene_6_p +NC_009143.1 NTv3 intron 131073 157033 . + . ID=gene_6_p_intron_131073;Parent=gene_6_p +NC_009143.1 NTv3 gene 139383 157033 . - . ID=gene_24_m +NC_009143.1 NTv3 CDS 139383 139386 . - 1 ID=gene_24_m_CDS_139383;Parent=gene_24_m +NC_009143.1 NTv3 intron 139387 157033 . - . 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"stop_codon": 2.1442240214346002 +} \ No newline at end of file diff --git a/metadata.tsv b/metadata.tsv new file mode 100644 index 0000000000000000000000000000000000000000..cb187617ed5f239257395cc512489bcc617524aa --- /dev/null +++ b/metadata.tsv @@ -0,0 +1,31 @@ +assembly species role tier source accession eval_chromosomes +GCF_000002775.5_P.trichocarpa_v4.1 Populus trichocarpa validation NCBI RefSeq GCF_000002775.5 NC_037293.2 +Tlatifoliav1.1 Typha latifolia validation JGI (GenBank copy) GCA_059706395.1 Chr15 +MguttatusvarIM62v3.1 Mimulus guttatus test JGI (GenBank copy) GCA_051942635.1 Chr_01 +GCF_003473485.1_MtrunA17r5.0-ANR Medicago truncatula test NCBI RefSeq GCF_003473485.1 NC_053047.1 +TAIR10 Arabidopsis thaliana train 1 Ensembl Plants (Araport11 genes) GCA_000001735.1 +GCF_000004075.3_Cucumber_9930_V3 Cucumis sativus train 1 NCBI RefSeq GCF_000004075.3 +GCF_022201045.2_DVS_A1.0 Citrus sinensis train 1 NCBI RefSeq GCF_022201045.2 +GCF_019578655.1_ASM1957865v1 Ricinus communis train 1 NCBI RefSeq GCF_019578655.1 +GCF_020921035.1_ASM2092103v1 Rhodamnia argentea train 1 NCBI RefSeq GCF_020921035.1 +GCF_005286985.2_Setaria_viridis_v4.0 Setaria viridis train 1 NCBI RefSeq GCF_005286985.2 +GCF_016808095.1_ASM1680809v1 Vigna angularis train 1 NCBI RefSeq GCF_016808095.1 +GCF_030704535.1_ASM3070453v1 Vitis vinifera train 1 NCBI RefSeq GCF_030704535.1 +GCF_031755915.1_ASM3175591v1 Ziziphus jujuba train 2 NCBI RefSeq GCF_031755915.1 +GCF_018687715.1_C.illinoinensisPawnee_v1 Carya illinoinensis train 2 NCBI RefSeq GCF_018687715.1 +GCF_036884655.1_Cavendish_Baxijiao_AAA Musa acuminata train 2 NCBI RefSeq GCF_036884655.1 +GCF_958298935.1_lpPhrAust1.1 Phragmites australis train 2 NCBI RefSeq GCF_958298935.1 +IRGSP-1.0 Oryza sativa train 2 Ensembl Plants genome, NCBI RefSeq genes GCF_001433935.1 +GCF_000309985.2_CAAS_Brap_v3.01 Brassica rapa train 3 NCBI RefSeq GCF_000309985.2 +GCF_025177605.1_USDA_Cmelo_AY_1.0 Cucumis melo train 3 NCBI RefSeq GCF_025177605.1 +GCF_002994745.2_RchiOBHm-V2 Rosa chinensis train 3 NCBI RefSeq GCF_002994745.2 +GCF_019419815.1_Pyrus_bretschneideri_v1 Pyrus bretschneideri train 3 NCBI RefSeq GCF_019419815.1 +GCF_042453785.1_GDT2T_hap1 Malus domestica train 3 NCBI RefSeq GCF_042453785.1 +GCF_937616625.2_ddMerAnnu1.2 Mercurialis annua train 3 NCBI RefSeq GCF_937616625.2 +GCF_963576675.1_ddEupLath1.1 Euphorbia lathyris train 3 NCBI RefSeq GCF_963576675.1 +GCF_020379485.1_Da-Ae Brassica napus train 3 NCBI RefSeq GCF_020379485.1 +GCF_030052815.1_ASM3005281v1 Hevea brasiliensis train 3 NCBI RefSeq GCF_030052815.1 +GCF_904849725.1_MorexV3_pseudomolecules_assembly Hordeum vulgare train 3 NCBI RefSeq GCF_904849725.1 +Zm-B73-REFERENCE-NAM-5.0 Zea mays train 3 Ensembl Plants genome, NCBI RefSeq genes GCF_902167145.1 +Gossypium_hirsutum_v2.1 Gossypium hirsutum train 3 NCBI RefSeq GCF_007990345.1 +Glycine_max_v2.1 Glycine max train 4 Ensembl Plants (INSDC genes) GCA_000004515.4