track multiz11cons
compositeTrack on
shortLabel Multiz 11-way
longLabel Multiz Alignment on 11 primate species
subGroup1 view Views align=Multiz_Alignments
dragAndDrop subTracks
visibility hide
type bed 4
group compGeno
html html/multiz11way

    track multiz11wayViewalign
    shortLabel Multiz 11-way
    view align
    visibility pack
    viewUi on
    subTrack multiz11cons

        track multiz11way
        subTrack multiz11wayViewalign
        shortLabel Multiz 11-way
        longLabel Multiz Alignment on 11 primate species
        subGroups view=align
        noInherit on
        type bigMaf
        viewUi on
        treeImage html/GCF_027406575.1_11way.png
        bigDataUrl bbi/GCF_027406575.1_mNycCou1.pri.multiz11way.bb
        summary bbi/GCF_027406575.1_mNycCou1.pri.multiz11waySummary.bb
        itemFirstCharCase noChange
        group compGeno
        color 0, 10, 100
        altColor 0,90,10
        speciesCodonDefault GCF_027406575.1
        speciesGroups Primates
        sGroup_Primates GCF_020740605.2 GCA_028858775.2 GCA_029289425.2 hg38 GCA_029281585.2 GCA_028885655.2 GCA_028885625.2 hs1 GCA_028878055.2 GCF_011100555.1 
        speciesLabels GCF_020740605.2="ring-tailed lemur" hg38="human/GRCh38.p14" GCF_027406575.1="slow loris" GCA_029281585.2="western lowland gorilla" GCA_029289425.2="pygmy chimpanzee" GCA_028858775.2="chimpanzee" GCA_028885655.2="Sumatran orangutan" GCA_028885625.2="Bornean orangutan" hs1="T2T CHM13v2.0" GCF_011100555.1="white-tufted-ear marmoset" GCA_028878055.2="siamang"

# don't have irows yet
#        irows on
# don't have frames yet
#        frames bbi/cactus11wayFrames.bb
#
# order.key.list:
# GCF_020740605.2	37.596	lastz.GCF_020740605.2/bigMaf/GCF_027406575.1.GCF_020740605.2.net.maf.gz
# GCA_028858775.2	16.270	lastz.GCA_028858775.2/bigMaf/GCF_027406575.1.GCA_028858775.2.net.maf.gz
# GCA_029289425.2	16.268	lastz.GCA_029289425.2/bigMaf/GCF_027406575.1.GCA_029289425.2.net.maf.gz
# hg38	16.254	lastz.hg38/bigMaf/GCF_027406575.1.hg38.net.maf.gz
# GCA_029281585.2	16.209	lastz.GCA_029281585.2/bigMaf/GCF_027406575.1.GCA_029281585.2.net.maf.gz
# GCA_028885655.2	16.201	lastz.GCA_028885655.2/bigMaf/GCF_027406575.1.GCA_028885655.2.net.maf.gz
# GCA_028885625.2	16.197	lastz.GCA_028885625.2/bigMaf/GCF_027406575.1.GCA_028885625.2.net.maf.gz
# hs1	16.154	lastz.hs1/bigMaf/GCF_027406575.1.hs1.net.maf.gz
# GCA_028878055.2	15.750	lastz.GCA_028878055.2/bigMaf/GCF_027406575.1.GCA_028878055.2.net.maf.gz
# GCF_011100555.1	12.281	lastz.GCF_011100555.1/bigMaf/GCF_027406575.1.GCF_011100555.1.net.maf.gz

# row counts in summary.bed
# 745838 GCA_028885655.2
# 745680 GCA_028885625.2
# 741785 GCA_028858775.2
# 741157 GCA_029281585.2
# 740233 GCA_029289425.2
# 739631 hg38
# 738674 hs1
# 728832 GCA_028878055.2
# 672353 GCF_011100555.1
# 558832 GCF_020740605.2

# GCF_020740605.2_mLemCat1.pri ring-tailed lemur (mLemCat1 2021)
# GCF_027406575.1_mNycCou1.pri slow loris (primary hap 2022)
# GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri western lowland gorilla (v2 KB3781 2024)
# GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri pygmy chimpanzee (v2 primary hap 2024)
# GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri chimpanzee (v2 AG18354 primary hap 2024)
# GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri Sumatran orangutan (v2 AG06213 primary hap 2024)
# GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri Bornean orangutan (v2 AG05252 primary hap 2024)
# GCF_011100555.1_mCalJa1.2.pat.X white-tufted-ear marmoset (v1.2 2021 refseq)
# GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri siamang (v2 Jambi primary hap 2024)