f1365818b0bbaf5b2c8ab01b848b26eec33be087 hiram Mon Jul 14 14:19:41 2025 -0700 Per advice from Francoise, do not override taxId for Bos indicus Bost taurus cross no redmine diff --git src/hg/makeDb/doc/asmHubs/sciNameOverride.txt src/hg/makeDb/doc/asmHubs/sciNameOverride.txt index fe019e974c7..f6ec38cd4f2 100644 --- src/hg/makeDb/doc/asmHubs/sciNameOverride.txt +++ src/hg/makeDb/doc/asmHubs/sciNameOverride.txt @@ -1,22 +1,24 @@ # override table for F1 cross hybrid assemblies where both haplotypes # are individual assemblies. Each individual assembly should have the # correct scientific species name (and subsequent) taxId for the actual # genome that it represents GCA_015852565.1 GCA_015852565.1_bf_hap-2 Branchiostoma floridae 7739 GCA_019207075.1 GCA_019207075.1_Bb-hap Branchiostoma belcheri 7741 -GCF_003369695.1 GCF_003369695.1_UOA_Brahman_1 Bos indicus 9915 -GCA_003369685.2 GCA_003369685.2_UOA_Angus_1 Bos taurus 9913 + +# Francoise says not to do this: they should both be taxId 30522 +# GCF_003369695.1 GCF_003369695.1_UOA_Brahman_1 Bos indicus 9915 +# GCA_003369685.2 GCA_003369685.2_UOA_Angus_1 Bos taurus 9913 # invertebrateAsmHub/invertebrate.orderList.tsv:GCA_019207075.1_Bb-hap lancelets B.floridae x B.belcheri (bbbf 2021) # invertebrateAsmHub/invertebrate.orderList.tsv:GCA_015852565.1_bf_hap-2 lancelets B.floridae x B.japonicum (bjbf 2020) # invertebrateAsmHub/invertebrate.orderList.tsv:GCF_000209225.1_ASM20922v1 starlet sea anemone (CH2 x CH6 2007 JGI) # mammalsAsmHub/mammals.orderList.tsv:GCA_003369685.2_UOA_Angus_1 hybrid cattle (Angus x Brahman F1 Angus haplotype 2018) # mammalsAsmHub/mammals.orderList.tsv:GCF_003369695.1_UOA_Brahman_1 hybrid cattle (Angus x Brahman F1 Brahman haplotype 2018) # mammalsAsmHub/mammals.orderList.tsv:GCF_029378745.1_NIAB-ARS_B.indTharparkar_mat_pri_1.0 zebu cattle (Sahiwal x Tharparkar maternal NIAB-ARS_2022 2023) # plantsAsmHub/plants.orderList.tsv:GCA_946000675.1_VITVix101-14Mgt_v1.0 eudicot V.riparia x Vitis rupestris (2022) # plantsAsmHub/plants.orderList.tsv:GCF_004785595.1_Jm3101_v1.0 J.microcarpa x regia eudicots (UCDavis 2019) # vgpAsmHub/vgp.alternate.orderList.tsv:GCA_003369685.2_UOA_Angus_1 hybrid cattle (Angus x Brahman F1 Angus haplotype 2018) # vgpAsmHub/vgp.primary.orderList.tsv:GCF_003369695.1_UOA_Brahman_1 hybrid cattle (Angus x Brahman F1 Brahman haplotype 2018) # vgpAsmHub/vgp.primary.orderList.tsv:GCA_019207075.1_Bb-hap lancelets B.floridae x B.belcheri (bbbf 2021) # vgpAsmHub/vgp.primary.orderList.tsv:GCA_015852565.1_bf_hap-2 lancelets B.floridae x B.japonicum (bjbf 2020)