344c5e2d07b4517677ea9a70fbededda133fc34f hiram Wed Aug 7 16:01:44 2024 -0700 VGP update with 48 added primary assemblies and 25 alternates refs #29545 diff --git src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt index 56a85b5..417b1df 100644 --- src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt +++ src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt @@ -134,30 +134,31 @@ 670352 GCA_017639475.1_bPluApr1.alt birds 670352 GCA_017639485.1_bPluApr1.pri birds 52777 GCA_017639555.1_bCicMag1.pri birds 148594 GCA_017639645.1_bFalNau1.mat birds 52777 GCA_017639665.1_bCicMag1.alt birds 946358 GCA_017639675.1_fAplTae1.pri fish 946358 GCA_017639685.1_fAplTae1.alt fish 1250792 GCA_017639755.1_fMelBoe1.alt fish 941984 GCA_017976295.1_fToxJac2.alt fish 55661 GCA_017976305.1_bCucCan1.alt birds 109905 GCA_017976315.1_fCheRos1.alt fish 55661 GCA_017976375.1_bCucCan1.pri birds 34773 GCA_018492705.1_fAloSap1.alt fish 2700040 GCA_019207075.1_Bb-hap invertebrate 33562 GCA_019395325.1_mDroGli1.alt mammals +27706 GCA_019677235.1_HNU_Msal_1.0 fish 75038 GCA_020382915.1_fScaArg1.alt fish 390368 GCA_020510965.1_fPhoLeu1.alt fish 390368 GCA_020510985.1_fPhoLeu1.pri fish 8895 GCA_020740585.1_bApuApu2.alt.cur birds 9447 GCA_020740595.1_mLemCat1.alt primates 134902 GCA_020740675.1_bCorHaw1.alt.cur birds 51337 GCA_020740715.1_mJacJac1.pat.decon mammals 8895 GCA_020740795.1_bApuApu2.pri.cur birds 34787 GCA_020745675.1_fTauAds1.alt.cur fish 34787 GCA_020745685.1_fTauAds1.pri.cur fish 243314 GCA_020745695.1_bHemCom1.alt.cur birds 243314 GCA_020745705.1_bHemCom1.pri.cur birds 170820 GCA_020745735.1_sHemOce1.pat.X.cur. sharks 170820 GCA_020745765.1_sHemOce1.mat.decon sharks 1118847 GCA_020745775.1_bTheCae1.pri.cur birds @@ -176,30 +177,31 @@ 345164 GCA_023634085.1_bFalChe1.pri birds 345164 GCA_023634115.1_bFalChe1.alt birds 8954 GCA_023634155.1_bFalPer1.pri birds 8954 GCA_023634185.1_bFalPer1.alt birds 345155 GCA_023634305.1_bFalBia1.alt birds 46513 GCA_023637925.1_DD_ASM_B1a birds 46513 GCA_023637945.1_DD_ASM_B1 birds 345155 GCA_023638135.1_bFalBia1.pri birds 48850 GCA_023851605.1_mTamTet1.pri mammals 48850 GCA_023853755.1_mTamTet1.alt mammals 109475 GCA_024140225.1_mSunEtr1.alt.cur mammals 99487 GCA_024166345.1_mEleMax1_alternate_haplotype mammals 9031 GCA_024206055.2_ASM2420605v2 birds 246179 GCA_024294585.1_rVipLat1.pri reptiles 246179 GCA_024294605.1_rVipLat1.alt reptiles +58319 GCA_024453875.1_ASM2445387v1 fish 10013 GCA_024803745.1_mThoBot1.0.p mammals 48708 GCA_025094165.1_mMesDen1_alternate_haplotype mammals 286002 GCA_025201965.1_rGopFla2.pat.asm reptiles 48708 GCA_025265405.1_mMesDen1_primary_haplotype mammals 70687 GCA_026018925.1_mTupTan1 mammals 372063 GCA_026229955.1_mPerMan1.0.p mammals 124745 GCA_026230045.1_mCorTow1.0.hap2 mammals 202280 GCA_026419925.1_bHarHar1 birds 27615 GCA_026419965.1_mKogBre1_haplotype_1 mammals 27615 GCA_026419985.1_mKogBre1_haplotype_2 mammals 8319 GCA_026652325.1_ASM2665232v1 amphibians 2997257 GCA_026936385.1_BBF_mMolNig1_v1 mammals 81927 GCA_026979555.1_bVidCha1_purged_dups_haplotype birds 81927 GCA_026979565.1_bVidCha1_merged_haplotype birds 65483 GCA_027172095.1_rPodRaf1.alt reptiles @@ -272,52 +274,54 @@ 9226 GCA_028858555.1_bAraAra1.hap2 birds 9117 GCA_028858595.1_bGruAme1.pat birds 57412 GCA_028858625.1_bColStr4.hap2 birds 57412 GCA_028858625.2_bColStr4.1.hap2 birds 57412 GCA_028858725.1_bColStr4.hap1 birds 9226 GCA_028858755.1_bAraAra1.hap1 birds 9598 GCA_028858805.1_NHGRI_mPanTro3-v1.1-hic.freeze_alt primates 9598 GCA_028858805.2_NHGRI_mPanTro3-v2.0_alt primates 9590 GCA_028878085.2_NHGRI_mSymSyn1-v2.0_alt primates 9600 GCA_028885525.1_NHGRI_mPonPyg2-v1.1-hic.freeze_alt primates 9600 GCA_028885525.2_NHGRI_mPonPyg2-v2.0_alt primates 9601 GCA_028885685.2_NHGRI_mPonAbe1-v2.0_alt primates 327740 GCA_029493135.1_aHylSar1.hap2 amphibians 2546036 GCA_029633845.1_fLamInc1.hap1 fish 27720 GCA_029633855.1_fHopMal1.hap1 fish +27720 GCA_029633855.2_fHopMal1.hap1 fish 27720 GCA_029633875.1_fHopMal1.hap2 fish 460621 GCA_029931755.1_rEulEur1.hap2 reptiles 9785 GCA_030014295.1_mLoxAfr1.hap2 mammals 2290929 GCA_030014385.1_fTriRos1.hap1 fish 2290929 GCA_030015355.1_fTriRos1.hap2 fish 94835 GCA_030020295.1_rGavGan2.hap2 reptiles 9785 GCA_030020305.1_mLoxAfr1.hap1 mammals 94835 GCA_030020385.1_rGavGan2.hap1 reptiles 143292 GCA_030020945.1_mManPen7.hap2 mammals 29137 GCA_030020955.1_mDugDug1.hap2 mammals 575201 GCA_030028035.1_mHipAmp2.hap1 mammals 1983395 GCA_030028105.1_sMobBir1.hap1 sharks 29137 GCA_030035585.1_mDugDug1.hap1 mammals 261503 GCA_030035675.1_rRhiFlo1.hap2 reptiles 1983395 GCA_030035685.1_sMobBir1.hap2 sharks 261503 GCA_030035715.1_rRhiFlo1.hap1 reptiles 79690 GCA_030144785.1_sHypSab1.hap2 sharks 79690 GCA_030144855.1_sHypSab1.hap1 sharks 118683 GCA_030412085.1_rCycPin1.hap2 reptiles 118683 GCA_030412105.1_rCycPin1.hap1 reptiles 9978 GCA_030435715.1_mOchPri1.hap2 mammals 9666 GCA_030435785.1_mMusLut2.alt mammals +187939 GCA_030440675.1_ASM3044067v1 reptiles 9361 GCA_030445055.1_mDasNov1.hap1 mammals 9361 GCA_030445055.2_mDasNov1.1.hap1 mammals 930266 GCA_030448965.1_fSalBra1.hap1 fish 36300 GCA_030449815.1_bPelCri1.alt birds 930266 GCA_030463535.1_fSalBra1.hap2 fish 36300 GCA_030463565.1_bPelCri1.pri birds 48891 GCA_030490855.1_bPoeAtr1.hap2 birds 3053191 GCA_030684295.1_sSteTig4.hap2 sharks 9823 GCA_030704935.1_ASM3070493v1 mammals 1192867 GCA_030820635.1_KIZ_Lrid_1.0 birds 9438 GCA_030848825.1_DD_mTadBra1_pri mammals 8496 GCA_030867065.1_rAllMis1 reptiles 283338 GCA_030867085.1_rLiaOli1.hap2 reptiles 283338 GCA_030867105.1_rLiaOli1.hap1 reptiles 30419 GCA_030867145.1_bOpiHoa1.hap1 birds @@ -337,30 +341,32 @@ 10013 GCA_031878665.1_mThoBot2.hap2 mammals 10013 GCA_031878675.1_mThoBot2.hap1 mammals 9802 GCA_031878705.1_mTapInd1.hap2 mammals 161624 GCA_031885435.1_bPasSan2.pri birds 238119 GCA_031893025.1_aLepFus1.hap1 amphibians 238119 GCA_031893055.1_aLepFus1.hap2 amphibians 142480 GCA_032164245.1_rSteOdo2_p1.0 reptiles 111125 GCA_032444005.1_aRanImi1.pri amphibians 3026461 GCA_033296515.1_rMacSuw1.hap1 reptiles 3026461 GCA_033349115.1_rMacSuw1.hap2 reptiles 44489 GCA_033958435.1_ASM3395843v1 reptiles 188344 GCA_034619455.1_bLepDis1.hap1 birds 188344 GCA_034619465.1_bLepDis1.hap2 birds 71010 GCA_035046495.1_rTilSci1.hap1 reptiles 71010 GCA_035046505.1_rTilSci1.hap2 reptiles +179887 GCA_035047305.1_BraPum1.0 reptiles +179890 GCA_035047345.1_BraVen1.1 reptiles 7740 GCA_035083965.1_klBraLanc5.hap2 invertebrate 7873 GCA_035084065.1_sHydCol1.hap1 sharks 212740 GCA_035084135.1_sHepPer1.hap2 sharks 212740 GCA_035084215.1_sHepPer1.hap1 sharks 7873 GCA_035084275.1_sHydCol1.hap2 sharks 51853 GCA_035125265.1_rCanAsp1.hap1 reptiles 51853 GCA_035149785.1_rCanAsp1.hap2 reptiles 7740 GCA_035149815.1_klBraLanc5.hap1 invertebrate 57060 GCA_035609135.1_aEleCoq1.hap2 amphibians 57060 GCA_035609145.1_aEleCoq1.hap1 amphibians 1914991 GCA_035770615.1_bMelMel2.pri birds 187106 GCA_036010745.1_bCalNic1.hap2 birds 8932 GCA_036010775.1_bColLiv1.mat birds 8932 GCA_036010775.2_bColLiv1.mat.v2 birds 3111550 GCA_036010785.1_bAmmMar1.pri birds @@ -392,47 +398,62 @@ 9796 GCA_036426135.1_mEquCab1.pat mammals 1570318 GCA_036850655.1_bMerOct1.hap2 birds 59482 GCA_036850765.1_mSacBil1_pri_phased_curated mammals 249018 GCA_036850995.1_mSacLep1_pri_phased_curated mammals 1570318 GCA_036873955.1_bMerOct1.hap1 birds 1343680 GCA_036971175.1_sNarBan1.hap2 sharks 1343680 GCA_036971445.1_sNarBan1.hap1 sharks 372321 GCA_036971685.1_bPatFas1.hap2 birds 10058 GCA_037038515.1_mMicPen1.hap1 mammals 249017 GCA_037038545.1_mRhyNas2.hap1 mammals 249017 GCA_037038555.1_mRhyNas2.hap2 mammals 54267 GCA_037038625.1_fFunDia1.hap2 fish 54267 GCA_037039145.1_fFunDia1.hap1 fish 10058 GCA_037039175.1_mMicPen1.hap2 mammals 1552295 GCA_037157525.1_mMolAlv2.hap1 mammals +678569 GCA_037157625.1_bLatDis1.hap2 birds 1552295 GCA_037176705.1_mMolAlv2.hap2 mammals 38937 GCA_037176765.1_rAnoSag1.mat reptiles 38937 GCA_037176775.1_rAnoSag1.pat reptiles 43566 GCA_037306005.1_aRhiDor1.hap1 amphibians 43566 GCA_037306015.1_aRhiDor1.hap2 amphibians +92651 GCA_037893015.1_bilby.v1.9.chrom.fasta mammals 43583 GCA_037950955.1_bSarPap1.hap2 birds 43583 GCA_037962945.1_bSarPap1.hap1 birds 28792 GCA_038021265.1_fCypVen1.hap1 fish 28792 GCA_038024135.1_fCypVen1.hap2 fish 3061075 GCA_038048845.1_aMixFle1.hap1 amphibians 3061075 GCA_038048865.1_aMixFle1.hap2 amphibians 8014 GCA_038355195.1_fOsmMor3.pri fish 27634 GCA_038363095.1_mArtLit.hap1 mammals +27634 GCA_038363095.2_mArtLit.hap1 mammals 51014 GCA_038363145.1_mArtInt1.hap1 mammals 51014 GCA_038363225.1_mArtInt1.hap2 mammals 288555 GCA_038501915.1_aXenPet1.maternal.cur amphibians 288555 GCA_038501925.1_aXenPet1.paternal.cur amphibians +2994998 GCA_039655065.1_mGloMut1.hap1 mammals +2994998 GCA_039656995.1_mGloMut1.hap2 mammals +151761 GCA_039720425.1_bAmaOch1.hap2 birds +151761 GCA_039720435.1_bAmaOch1.hap1 birds +109706 GCA_039877575.1_fChaTrf1.hap2 fish +109706 GCA_039877785.1_fChaTrf1.hap1 fish +46218 GCA_039878515.1_bCotChi1.hap1 birds +46218 GCA_039878825.1_bCotChi1.hap2 birds +48277 GCA_039906465.1_bAegAlb1.hap2 birds +82174 GCA_039906515.1_mPseCra1.hap1 mammals +82174 GCA_039906525.1_mPseCra1.hap2 mammals +48277 GCA_039906565.1_bAegAlb1.hap1 birds 8154 GCA_900246225.5_fAstCal1.3 fish 64144 GCA_900324465.2_fAnaTes1.2 fish 64144 GCA_900324465.3_fAnaTes1.3 fish 205130 GCA_900324485.3_fMasArm1.3 fish 56716 GCA_900634415.1_fCotGob3.1 fish 56716 GCA_900634435.1_fCotGob3.1_alternate_haplotype fish 210632 GCA_900634625.2_fParRan2.2 fish 441366 GCA_900634775.1_fGouWil2.1 fish 441366 GCA_900634775.2_fGouWil2.2 fish 64144 GCA_900650485.1_fAnaTes1.2_alternate_haplotype fish 441366 GCA_900650505.1_fGouWil2.1_alternate_haplotype fish 210632 GCA_900651595.1_fParRan2.1_alternate_haplotype fish 158456 GCA_900651605.1_fBetSpl5.1_alternate_haplotype fish 158456 GCA_900651605.2_fBetSpl5.4_alternate_haplotype fish 299321 GCA_900700345.2_fDenClu1.1_alternate_haplotype fish @@ -615,42 +636,86 @@ 37598 GCA_963513975.1_bFriCoe1.1 birds 223862 GCA_963514005.1_sRajBra1.1 sharks 48171 GCA_963514085.1_fCheLab1.1 fish 426098 GCA_963514095.1_fEutGur1.1 fish 127875 GCA_963662255.1_bCinCin1.1 birds 94984 GCA_963691815.1_fEchVip8.1 fish 13677 GCA_963691925.1_fScoSco1.1 fish 29151 GCA_963692335.1_fOsmEpe2.1 fish 27697 GCA_963854185.1_fSarPil1.1 fish 52904 GCA_963854745.1_fScoMax1.1 fish 473322 GCA_963921795.1_fNanAch1.1 fish 9209 GCA_963921805.1_bPhaCar2.1 birds 443714 GCA_963924005.1_fProBol1.1 fish 1192867 GCA_963924245.1_bChrRid1.1 birds 59485 GCA_963924515.1_mVesMur1.1 mammals +201961 GCA_963924565.1_kaAscAspe10.1 otherChordates 13151 GCA_963924665.1_mMicMin1.1 mammals 9742 GCA_963924675.1_mPhoPho1.1 mammals 8237 GCA_963924715.1_fThuThy2.1 fish 9886 GCA_963930665.1_mMunRee1.1_alternate_haplotype mammals 56723 GCA_963930695.1_fLabBer1.1 fish 28680 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