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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.14

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-02-05, 13:06 CET based on data in: /data/medugorac/Shared/Maulik/projects/scalePopgen/work/90/c75af367a615a52b019b2459cd1cce

        summary statistics

        summary statistics of individual sample and population.

        Population-wise distribution of Expected heterozygosity

        Distribution of expected heterozygosity in a user-defined window

        Population-wise distribution of observed heterozygosity

        Distribution of observed heterozygosity in a user-defined window

        Population-wise distribution of minor allele frequency

        Distribution of mean minor allele frequency in a user-defined window

        Sample-wise summary statistics of SNP counts

        The SNP counts are calculated using plink2

        Bokeh Plot

        Genetic structure

        analysis carried out to explore genetic structure of populations.

        Identical by state (IBS) distance based Neighbor Joining (NJ) tree

        1-IBS distance was calculated using plink and NJ distances were calculated using Biopyton module

        idx: 0 dist: 0.0644 support: 0.0000 height: 0.0125 pop: Holstein name: SRS597739idx: 1 dist: 0.0701 support: 0.0000 height: 0.0068 pop: Holstein name: SRS597741idx: 2 dist: 0.0846 support: 0.0000 height: 0.0018 pop: Holstein name: SRS597750idx: 3 dist: 0.0833 support: 0.0000 height: 0.0132 pop: Holstein name: SRS597749idx: 4 dist: 0.0952 support: 0.0000 height: 0.0060 pop: Holstein name: SRS597742idx: 5 dist: 0.0907 support: 0.0000 height: 0.0166 pop: Holstein name: SRS597729idx: 6 dist: 0.0758 support: 0.0000 height: 0.0152 pop: Holstein name: SRS582840idx: 7 dist: 0.0778 support: 0.0000 height: 0.0133 pop: Holstein name: SRS582855idx: 8 dist: 0.0673 support: 0.0000 height: 0.0115 pop: Holstein name: SRS597736idx: 9 dist: 0.0675 support: 0.0000 height: 0.0113 pop: Holstein name: SRS597744idx: 10 dist: 0.0923 support: 0.0000 height: 0.0178 pop: Holstein name: SRS597746idx: 11 dist: 0.0905 support: 0.0000 height: 0.0110 pop: Holstein name: SRS597732idx: 12 dist: 0.0827 support: 0.0000 height: 0.0188 pop: Holstein name: SRS597735idx: 13 dist: 0.0700 support: 0.0000 height: 0.0099 pop: Holstein name: SRS597733idx: 14 dist: 0.0707 support: 0.0000 height: 0.0093 pop: Holstein name: SRS597740idx: 15 dist: 0.0860 support: 0.0000 height: 0.0101 pop: Holstein name: SRS597737idx: 16 dist: 0.0840 support: 0.0000 height: 0.0121 pop: Holstein name: SRS597743idx: 17 dist: 0.0898 support: 0.0000 height: 0.0117 pop: Holstein name: SRS597730idx: 18 dist: 0.0836 support: 0.0000 height: 0.0179 pop: Holstein name: SRS597752idx: 19 dist: 0.0895 support: 0.0000 height: 0.0182 pop: Holstein name: SRS597753idx: 20 dist: 0.1046 support: 0.0000 height: 0.0025 pop: Holstein name: SRS565647idx: 21 dist: 0.0915 support: 0.0000 height: 0.0155 pop: Holstein name: SRS597748idx: 22 dist: 0.0869 support: 0.0000 height: 0.0178 pop: Holstein name: SRS597747idx: 23 dist: 0.0892 support: 0.0000 height: 0.0155 pop: Holstein name: SRS597755idx: 24 dist: 0.1054 support: 0.0000 height: 0.0056 pop: Holstein name: SRS565646idx: 25 dist: 0.1110 support: 0.0000 height: 0.0036 pop: Holstein name: SRS565648idx: 26 dist: 0.0830 support: 0.0000 height: 0.0166 pop: Holstein name: SRS565374idx: 27 dist: 0.0863 support: 0.0000 height: 0.0132 pop: Holstein name: SRS597751idx: 28 dist: 0.0858 support: 0.0000 height: 0.0201 pop: Kholmogory name: SRS6910408idx: 29 dist: 0.0878 support: 0.0000 height: 0.0181 pop: Kholmogory name: SRS6910420idx: 30 dist: 0.0878 support: 0.0000 height: 0.0208 pop: Kholmogory name: SRS6910386idx: 31 dist: 0.0906 support: 0.0000 height: 0.0164 pop: Kholmogory name: SRS6910390idx: 32 dist: 0.0872 support: 0.0000 height: 0.0198 pop: Kholmogory name: SRS6910396idx: 33 dist: 0.0891 support: 0.0000 height: 0.0191 pop: Kholmogory name: SRS6910421idx: 34 dist: 0.0916 support: 0.0000 height: 0.0165 pop: Kholmogory name: SRS6910422idx: 35 dist: 0.0919 support: 0.0000 height: 0.0180 pop: Kholmogory name: SRS6910388idx: 36 dist: 0.0922 support: 0.0000 height: 0.0192 pop: Kholmogory name: SRS6910391idx: 37 dist: 0.0931 support: 0.0000 height: 0.0193 pop: Kholmogory name: SRS6910419idx: 38 dist: 0.0863 support: 0.0000 height: 0.0199 pop: Kholmogory name: SRS6910389idx: 39 dist: 0.0876 support: 0.0000 height: 0.0186 pop: Kholmogory name: SRS6910397idx: 40 dist: 0.0882 support: 0.0000 height: 0.0201 pop: Kholmogory name: SRS6910394idx: 41 dist: 0.0870 support: 0.0000 height: 0.0184 pop: Kholmogory name: SRS6910392idx: 42 dist: 0.0849 support: 0.0000 height: 0.0204 pop: Kholmogory name: SRS6910424idx: 43 dist: 0.0920 support: 0.0000 height: 0.0182 pop: Kholmogory name: SRS6910387idx: 44 dist: 0.0886 support: 0.0000 height: 0.0190 pop: Kholmogory name: SRS6910385idx: 45 dist: 0.0897 support: 0.0000 height: 0.0180 pop: Kholmogory name: SRS6910423idx: 46 dist: 0.0969 support: 0.0000 height: 0.0163 pop: Kholmogory name: SRS6910393idx: 47 dist: 0.0958 support: 0.0000 height: 0.0175 pop: Kholmogory name: SRS6910395idx: 48 dist: 0.0688 support: 0.0000 height: 0.0165 pop: Hereford name: SRS629095idx: 49 dist: 0.0675 support: 0.0000 height: 0.0178 pop: Hereford name: SRS629340idx: 50 dist: 0.0759 support: 0.0000 height: 0.0178 pop: Hereford name: SRS629099idx: 51 dist: 0.0780 support: 0.0000 height: 0.0156 pop: Hereford name: SRS631191idx: 52 dist: 0.0819 support: 0.0000 height: 0.0171 pop: Hereford name: SRS629339idx: 53 dist: 0.0838 support: 0.0000 height: 0.0161 pop: Hereford name: SRS629097idx: 54 dist: 0.0718 support: 0.0000 height: 0.0197 pop: Hereford name: SRS629694idx: 55 dist: 0.0753 support: 0.0000 height: 0.0162 pop: Hereford name: SRS631192idx: 56 dist: 0.0785 support: 0.0000 height: 0.0156 pop: Hereford name: SRS631194idx: 57 dist: 0.0801 support: 0.0000 height: 0.0178 pop: Hereford name: SRS631208idx: 58 dist: 0.0848 support: 0.0000 height: 0.0159 pop: Hereford name: SRS629094idx: 59 dist: 0.0966 support: 0.0000 height: 0.0068 pop: Hereford name: SRS428710idx: 60 dist: 0.0703 support: 0.0000 height: 0.0185 pop: Hereford name: SRS629092idx: 61 dist: 0.0728 support: 0.0000 height: 0.0160 pop: Hereford name: SRS631190idx: 62 dist: 0.0736 support: 0.0000 height: 0.0205 pop: Hereford name: SRS631226idx: 63 dist: 0.0930 support: 0.0000 height: 0.0050 pop: Hereford name: SRS428704idx: 64 dist: 0.0817 support: 0.0000 height: 0.0192 pop: Hereford name: SRS631198idx: 65 dist: 0.0817 support: 0.0000 height: 0.0192 pop: Hereford name: SRS631223idx: 66 dist: 0.0804 support: 0.0000 height: 0.0203 pop: Hereford name: SRS631211idx: 67 dist: 0.0823 support: 0.0000 height: 0.0185 pop: Hereford name: SRS631216idx: 68 dist: 0.0824 support: 0.0000 height: 0.0189 pop: Hereford name: SRS631213idx: 69 dist: 0.0872 support: 0.0000 height: 0.0164 pop: Hereford name: SRS628362idx: 70 dist: 0.0858 support: 0.0000 height: 0.0200 pop: Hereford name: SRS631195idx: 71 dist: 0.0761 support: 0.0000 height: 0.0259 pop: Hereford name: SRS631218idx: 72 dist: 0.0879 support: 0.0000 height: 0.0142 pop: Hereford name: SRS631225idx: 73 dist: 0.0869 support: 0.0000 height: 0.0180 pop: Hereford name: SRS631224idx: 74 dist: 0.0968 support: 0.0000 height: 0.0123 pop: Hereford name: SRS428705idx: 75 dist: 0.0643 support: 0.0000 height: 0.0133 pop: Jersey name: SRS597765idx: 76 dist: 0.0689 support: 0.0000 height: 0.0086 pop: Jersey name: SRS597766idx: 77 dist: 0.0641 support: 0.0000 height: 0.0136 pop: Jersey name: SRS597768idx: 78 dist: 0.0690 support: 0.0000 height: 0.0086 pop: Jersey name: SRS597769idx: 79 dist: 0.0633 support: 0.0000 height: 0.0070 pop: Jersey name: SRS597762idx: 80 dist: 0.0642 support: 0.0000 height: 0.0061 pop: Jersey name: SRS597767idx: 81 dist: 0.0916 support: 0.0000 height: 0.0015 pop: Jersey name: SRS597761idx: 82 dist: 0.0805 support: 0.0000 height: 0.0000 pop: Jersey name: SRS597763idx: 83 dist: 0.0669 support: 0.0000 height: 0.0135 pop: Jersey name: SRS597770idx: 84 dist: 0.0835 support: 0.0000 height: 0.0100 pop: Jersey name: SRS597764idx: 85 dist: 0.0897 support: 0.0000 height: 0.0111 pop: Jersey name: SRS597758idx: 86 dist: 0.0852 support: 0.0000 height: 0.0156 pop: Jersey name: SRS597760idx: 87 dist: 0.0996 support: 0.0000 height: 0.0038 pop: Jersey name: SRS597759idx: 88 dist: 0.0933 support: 0.0000 height: 0.0110 pop: Jersey name: SRS597756idx: 89 dist: 0.0940 support: 0.0000 height: 0.0103 pop: Jersey name: SRS597757idx: 90 dist: 0.0785 support: 0.0000 height: 0.0049 pop: Angus name: SRS597602idx: 91 dist: 0.0733 support: 0.0000 height: 0.0100 pop: Angus name: SRS597608idx: 92 dist: 0.0721 support: 0.0000 height: 0.0132 pop: Angus name: SRS597621idx: 93 dist: 0.0683 support: 0.0000 height: 0.0169 pop: Angus name: SRS597625idx: 94 dist: 0.0772 support: 0.0000 height: 0.0111 pop: Angus name: SRS597604idx: 95 dist: 0.0700 support: 0.0000 height: 0.0183 pop: Angus name: SRS597617idx: 96 dist: 0.0757 support: 0.0000 height: 0.0119 pop: Angus name: SRS597616idx: 97 dist: 0.0707 support: 0.0000 height: 0.0169 pop: Angus name: SRS597622idx: 98 dist: 0.0750 support: 0.0000 height: 0.0112 pop: Angus name: SRS597609idx: 99 dist: 0.0757 support: 0.0000 height: 0.0106 pop: Angus name: SRS597614idx: 100 dist: 0.0790 support: 0.0000 height: 0.0091 pop: Angus name: SRS597613idx: 101 dist: 0.0768 support: 0.0000 height: 0.0121 pop: Angus name: SRS597624idx: 102 dist: 0.0917 support: 0.0000 height: 0.0085 pop: Angus name: SRS597626idx: 103 dist: 0.0833 support: 0.0000 height: 0.0062 pop: Angus name: SRS597597idx: 104 dist: 0.0774 support: 0.0000 height: 0.0120 pop: Angus name: SRS597618idx: 105 dist: 0.0801 support: 0.0000 height: 0.0099 pop: Angus name: SRS597611idx: 106 dist: 0.0743 support: 0.0000 height: 0.0157 pop: Angus name: SRS597623idx: 107 dist: 0.0746 support: 0.0000 height: 0.0098 pop: Angus name: SRS597601idx: 108 dist: 0.0756 support: 0.0000 height: 0.0088 pop: Angus name: SRS597620idx: 109 dist: 0.0838 support: 0.0000 height: 0.0040 pop: Angus name: SRS597598idx: 110 dist: 0.0729 support: 0.0000 height: 0.0158 pop: Angus name: SRS597605idx: 111 dist: 0.0751 support: 0.0000 height: 0.0053 pop: Angus name: SRS597595idx: 112 dist: 0.0689 support: 0.0000 height: 0.0114 pop: Angus name: SRS597607idx: 113 dist: 0.0764 support: 0.0000 height: 0.0111 pop: Angus name: SRS597610idx: 114 dist: 0.0755 support: 0.0000 height: 0.0119 pop: Angus name: SRS614728idx: 115 dist: 0.0657 support: 0.0000 height: 0.0199 pop: Angus name: SRS597615idx: 116 dist: 0.0699 support: 0.0000 height: 0.0156 pop: Angus name: SRS597619idx: 117 dist: 0.0728 support: 0.0000 height: 0.0164 pop: Angus name: SRS597612idx: 118 dist: 0.0771 support: 0.0000 height: 0.0125 pop: Angus name: SRS597606idx: 119 dist: 0.0792 support: 0.0000 height: 0.0114 pop: Angus name: SRS597603idx: 120 dist: 0.0862 support: 0.0000 height: 0.0096 pop: Red_Angus name: SRS428708idx: 121 dist: 0.0747 support: 0.0000 height: 0.0211 pop: Red_Angus name: SRS641741idx: 122 dist: 0.0881 support: 0.0000 height: 0.0118 pop: Red_Angus name: SRS428709idx: 123 dist: 0.0866 support: 0.0000 height: 0.0189 pop: Red_Angus name: SRS629338idx: 124 dist: 0.0853 support: 0.0000 height: 0.0203 pop: Red_Angus name: SRS641737idx: 125 dist: 0.0877 support: 0.0000 height: 0.0200 pop: Red_Angus name: SRS628373idx: 126 dist: 0.0881 support: 0.0000 height: 0.0207 pop: Red_Angus name: SRS628374idx: 127 dist: 0.0881 support: 0.0000 height: 0.0219 pop: Red_Angus name: SRS641736idx: 128 dist: 0.0873 support: 0.0000 height: 0.0200 pop: Red_Angus name: SRS631187idx: 129 dist: 0.0858 support: 0.0000 height: 0.0215 pop: Red_Angus name: SRS631188idx: 130 dist: 0.0910 support: 0.0000 height: 0.0190 pop: Red_Angus name: SRS629341idx: 131 dist: 0.0868 support: 0.0000 height: 0.0232 pop: Red_Angus name: SRS631196idx: 132 dist: 0.0879 support: 0.0000 height: 0.0225 pop: Red_Angus name: SRS629672idx: 133 dist: 0.0855 support: 0.0000 height: 0.0243 pop: Maine_Anjou name: SRS629671idx: 134 dist: 0.0842 support: 0.0000 height: 0.0256 pop: Maine_Anjou name: SRS631210idx: 135 dist: 0.0877 support: 0.0000 height: 0.0239 pop: Maine_Anjou name: SRS631215idx: 136 dist: 0.0881 support: 0.0000 height: 0.0248 pop: Maine_Anjou name: SRS631212idx: 137 dist: 0.0881 support: 0.0000 height: 0.0245 pop: Maine_Anjou name: SRS629678idx: 138 dist: 0.0883 support: 0.0000 height: 0.0243 pop: Maine_Anjou name: SRS631193idx: 139 dist: 0.0888 support: 0.0000 height: 0.0244 pop: Maine_Anjou name: SRS629692idx: 140 dist: 0.0903 support: 0.0000 height: 0.0248 pop: Charolais name: SRS629686idx: 141 dist: 0.0876 support: 0.0000 height: 0.0274 pop: Charolais name: SRS631230idx: 142 dist: 0.0942 support: 0.0000 height: 0.0261 pop: Charolais name: SRS629691idx: 143 dist: 0.0961 support: 0.0000 height: 0.0247 pop: Charolais name: SRS628370idx: 144 dist: 0.0963 support: 0.0000 height: 0.0237 pop: Charolais name: SRS628372idx: 145 dist: 0.0941 support: 0.0000 height: 0.0260 pop: Charolais name: SRS629321idx: 146 dist: 0.0941 support: 0.0000 height: 0.0252 pop: Charolais name: SRS628369idx: 147 dist: 0.0955 support: 0.0000 height: 0.0238 pop: Charolais name: SRS629334idx: 148 dist: 0.0975 support: 0.0000 height: 0.0240 pop: Charolais name: SRS628371idx: 149 dist: 0.0968 support: 0.0000 height: 0.0237 pop: Charolais name: SRS628376idx: 150 dist: 0.0943 support: 0.0000 height: 0.0263 pop: Charolais name: SRS631207idx: 151 dist: 0.0976 support: 0.0000 height: 0.0235 pop: Charolais name: SRS629687idx: 152 dist: 0.0766 support: 0.0000 height: 0.0120 pop: Simmental name: SRS597774idx: 153 dist: 0.0746 support: 0.0000 height: 0.0140 pop: Simmental name: SRS597788idx: 154 dist: 0.0816 support: 0.0000 height: 0.0164 pop: Simmental name: SRS597781idx: 155 dist: 0.0978 support: 0.0000 height: 0.0109 pop: Simmental name: SRS597809idx: 156 dist: 0.0995 support: 0.0000 height: 0.0147 pop: Simmental name: SRS597782idx: 157 dist: 0.1001 support: 0.0000 height: 0.0142 pop: Simmental name: SRS597811idx: 158 dist: 0.0974 support: 0.0000 height: 0.0101 pop: Simmental name: SRS597797idx: 159 dist: 0.0933 support: 0.0000 height: 0.0143 pop: Simmental name: SRS597808idx: 160 dist: 0.1008 support: 0.0000 height: 0.0118 pop: Simmental name: SRS597776idx: 161 dist: 0.1002 support: 0.0000 height: 0.0164 pop: Simmental name: SRS597778idx: 162 dist: 0.0923 support: 0.0000 height: 0.0156 pop: Simmental name: SRS597792idx: 163 dist: 0.0936 support: 0.0000 height: 0.0143 pop: Simmental name: SRS597812idx: 164 dist: 0.0927 support: 0.0000 height: 0.0190 pop: Simmental name: SRS597775idx: 165 dist: 0.0875 support: 0.0000 height: 0.0174 pop: Simmental name: SRS597780idx: 166 dist: 0.0916 support: 0.0000 height: 0.0133 pop: Simmental name: SRS597796idx: 167 dist: 0.0857 support: 0.0000 height: 0.0170 pop: Simmental name: SRS597785idx: 168 dist: 0.0852 support: 0.0000 height: 0.0175 pop: Simmental name: SRS597798idx: 169 dist: 0.0938 support: 0.0000 height: 0.0139 pop: Simmental name: SRS597795idx: 170 dist: 0.0851 support: 0.0000 height: 0.0162 pop: Simmental name: SRS597787idx: 171 dist: 0.0886 support: 0.0000 height: 0.0127 pop: Simmental name: SRS597791idx: 172 dist: 0.0915 support: 0.0000 height: 0.0166 pop: Simmental name: SRS597773idx: 173 dist: 0.0971 support: 0.0000 height: 0.0109 pop: Simmental name: SRS597777idx: 174 dist: 0.0902 support: 0.0000 height: 0.0249 pop: Simmental name: SRS597772idx: 175 dist: 0.0972 support: 0.0000 height: 0.0206 pop: Simmental name: SRS597786idx: 176 dist: 0.1031 support: 0.0000 height: 0.0158 pop: Simmental name: SRS597813idx: 177 dist: 0.0779 support: 0.0000 height: 0.0132 pop: Simmental name: SRS597794idx: 178 dist: 0.0713 support: 0.0000 height: 0.0198 pop: Simmental name: SRS597799idx: 179 dist: 0.0854 support: 0.0000 height: 0.0126 pop: Simmental name: SRS597789idx: 180 dist: 0.0914 support: 0.0000 height: 0.0119 pop: Simmental name: SRS597771idx: 181 dist: 0.0767 support: 0.0000 height: 0.0213 pop: Gelbvieh name: SRS628363idx: 182 dist: 0.0725 support: 0.0000 height: 0.0255 pop: Gelbvieh name: SRS631197idx: 183 dist: 0.0916 support: 0.0000 height: 0.0219 pop: Gelbvieh name: SRS629683idx: 184 dist: 0.0837 support: 0.0000 height: 0.0277 pop: Gelbvieh name: SRS628367idx: 185 dist: 0.0858 support: 0.0000 height: 0.0257 pop: Gelbvieh name: SRS629693idx: 186 dist: 0.0819 support: 0.0000 height: 0.0247 pop: Gelbvieh name: SRS629100idx: 187 dist: 0.0833 support: 0.0000 height: 0.0233 pop: Gelbvieh name: SRS629679idx: 188 dist: 0.0840 support: 0.0000 height: 0.0252 pop: Gelbvieh name: SRS629673idx: 189 dist: 0.0895 support: 0.0000 height: 0.0254 pop: Gelbvieh name: SRS629326idx: 190 dist: 0.0819 support: 0.0000 height: 0.0233 pop: Gelbvieh name: SRS629675idx: 191 dist: 0.0805 support: 0.0000 height: 0.0248 pop: Gelbvieh name: SRS629681idx: 192 dist: 0.0912 support: 0.0000 height: 0.0251 pop: Gelbvieh name: SRS629674idx: 193 dist: 0.0809 support: 0.0000 height: 0.0262 pop: Gelbvieh name: SRS629676idx: 194 dist: 0.0842 support: 0.0000 height: 0.0230 pop: Gelbvieh name: SRS631221idx: 195 dist: 0.0968 support: 0.0000 height: 0.0242 pop: Gelbvieh name: SRS628366idx: 196 dist: 0.0947 support: 0.0000 height: 0.0236 pop: Gelbvieh name: SRS628364idx: 197 dist: 0.0963 support: 0.0000 height: 0.0220 pop: Gelbvieh name: SRS629669idx: 198 dist: 0.0959 support: 0.0000 height: 0.0195 pop: Gelbvieh name: SRS628368idx: 199 dist: 0.0905 support: 0.0000 height: 0.0249 pop: Gelbvieh name: SRS641742idx: 200 dist: 0.0926 support: 0.0000 height: 0.0243 pop: Gelbvieh name: SRS629682idx: 201 dist: 0.0943 support: 0.0000 height: 0.0237 pop: Gelbvieh name: SRS629325idx: 202 dist: 0.0950 support: 0.0000 height: 0.0253 pop: Gelbvieh name: SRS629684idx: 203 dist: 0.0964 support: 0.0000 height: 0.0333 pop: Kazakh_Cattle name: SRS2165153idx: 204 dist: 0.0964 support: 0.0000 height: 0.0334 pop: Kazakh_Cattle name: SRS2165154idx: 205 dist: 0.0977 support: 0.0000 height: 0.0333 pop: Kazakh_Cattle name: SRS2165155idx: 206 dist: 0.0836 support: 0.0000 height: 0.0321 pop: Kazakh_Cattle name: SRS2165147idx: 207 dist: 0.0834 support: 0.0000 height: 0.0323 pop: Kazakh_Cattle name: SRS2165149idx: 208 dist: 0.1092 support: 0.0000 height: 0.0206 pop: Kazakh_Cattle name: SRS2165150idx: 209 dist: 0.0981 support: 0.0000 height: 0.0334 pop: Kazakh_Cattle name: SRS2165148idx: 210 dist: 0.0991 support: 0.0000 height: 0.0329 pop: Kazakh_Cattle name: SRS2165151idx: 211 dist: 0.1006 support: 0.0000 height: 0.0323 pop: Kazakh_Cattle name: SRS2165152idx: 212 dist: 0.0834 support: 0.0000 height: 0.0349 pop: Mongolian_Cattle name: SRS2165157idx: 213 dist: 0.0828 support: 0.0000 height: 0.0356 pop: Mongolian_Cattle name: SRS2165160idx: 214 dist: 0.0988 support: 0.0000 height: 0.0359 pop: Mongolian_Cattle name: SRS2165156idx: 215 dist: 0.0644 support: 0.0000 height: 0.0257 pop: Yakut name: SRS6910398idx: 216 dist: 0.0600 support: 0.0000 height: 0.0300 pop: Yakut name: SRS6910406idx: 217 dist: 0.0597 support: 0.0000 height: 0.0285 pop: Yakut name: SRS6910409idx: 218 dist: 0.0617 support: 0.0000 height: 0.0265 pop: Yakut name: SRS6910412idx: 219 dist: 0.0658 support: 0.0000 height: 0.0277 pop: Yakut name: SRS6910401idx: 220 dist: 0.0636 support: 0.0000 height: 0.0300 pop: Yakut name: SRS6910411idx: 221 dist: 0.0741 support: 0.0000 height: 0.0294 pop: Yakut name: SRS6910400idx: 222 dist: 0.0774 support: 0.0000 height: 0.0313 pop: Yakut name: SRS6910399idx: 223 dist: 0.0699 support: 0.0000 height: 0.0309 pop: Yakut name: SRS6910402idx: 224 dist: 0.0754 support: 0.0000 height: 0.0255 pop: Yakut name: SRS6910417idx: 225 dist: 0.0649 support: 0.0000 height: 0.0300 pop: Yakut name: SRS6910414idx: 226 dist: 0.0649 support: 0.0000 height: 0.0300 pop: Yakut name: SRS6910415idx: 227 dist: 0.0790 support: 0.0000 height: 0.0290 pop: Yakut name: SRS6910403idx: 228 dist: 0.0775 support: 0.0000 height: 0.0313 pop: Yakut name: SRS6910407idx: 229 dist: 0.0822 support: 0.0000 height: 0.0266 pop: Yakut name: SRS6910418idx: 230 dist: 0.0827 support: 0.0000 height: 0.0299 pop: Yakut name: SRS6910405idx: 231 dist: 0.0823 support: 0.0000 height: 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0.1195 pop: name: Inner94idx: 503 dist: 0.0013 support: 0.0000 height: 0.1334 pop: name: Inner181idx: 504 dist: 0.0037 support: 0.0000 height: 0.1195 pop: name: Inner61idx: 505 dist: 0.0014 support: 0.0000 height: 0.1179 pop: name: Inner7idx: 506 dist: 0.0120 support: 0.0000 height: 0.1400 pop: name: Inner10idx: 507 dist: 0.0049 support: 0.0000 height: 0.1423 pop: name: Inner15idx: 508 dist: 0.0011 support: 0.0000 height: 0.1486 pop: name: Inner2idx: 509 dist: 0.0016 support: 0.0000 height: 0.1361 pop: name: Inner222idx: 510 dist: 0.0030 support: 0.0000 height: 0.1347 pop: name: Inner199idx: 511 dist: 0.0059 support: 0.0000 height: 0.1232 pop: name: Inner85idx: 512 dist: 0.0105 support: 0.0000 height: 0.1186 pop: name: Inner59idx: 513 dist: 0.0045 support: 0.0000 height: 0.1194 pop: name: Inner8idx: 514 dist: 0.0012 support: 0.0000 height: 0.1227 pop: name: Inner14idx: 515 dist: 0.0122 support: 0.0000 height: 0.1096 pop: name: Inner1idx: 516 dist: 0.0015 support: 0.0000 height: 0.1520 pop: name: Inner27idx: 517 dist: 0.0063 support: 0.0000 height: 0.1472 pop: name: Inner20idx: 518 dist: 0.0027 support: 0.0000 height: 0.1501 pop: name: Inner25idx: 519 dist: 0.0022 support: 0.0000 height: 0.1497 pop: name: Inner3idx: 520 dist: 0.0018 support: 0.0000 height: 0.1377 pop: name: Inner210idx: 521 dist: 0.0104 support: 0.0000 height: 0.1291 pop: name: Inner104idx: 522 dist: 0.0011 support: 0.0000 height: 0.1239 pop: name: Inner16idx: 523 dist: 0.0032 support: 0.0000 height: 0.1218 pop: name: Inner12idx: 524 dist: 0.0004 support: 0.0000 height: 0.1535 pop: name: Inner32idx: 525 dist: 0.0012 support: 0.0000 height: 0.1528 pop: name: Inner29idx: 526 dist: 0.0013 support: 0.0000 height: 0.1519 pop: name: Inner4idx: 527 dist: 0.0126 support: 0.0000 height: 0.1395 pop: name: Inner205idx: 528 dist: 0.0271 support: 0.0000 height: 0.1250 pop: name: Inner18idx: 529 dist: 0.0011 support: 0.0000 height: 0.1539 pop: name: Inner33idx: 530 dist: 0.0014 support: 0.0000 height: 0.1532 pop: name: Inner5idx: 531 dist: 0.0098 support: 0.0000 height: 0.1521 pop: name: Inner93idx: 532 dist: 0.0069 support: 0.0000 height: 0.1550 pop: name: Inner34idx: 533 dist: 0.0073 support: 0.0000 height: 0.1546 pop: name: Inner6idx: 534 dist: 0.0101 support: 1.0000 height: 0.1619 pop: name: Inner51idx: 535 dist: 0.0101 support: 0.0000 height: 0.1619 pop: name: Inner13idx: 536 dist: 1.0000 support: 1.0000 height: 0.1720 pop: name: rootSRS597739SRS597741SRS597750SRS597749SRS597742SRS597729SRS582840SRS582855SRS597736SRS597744SRS597746SRS597732SRS597735SRS597733SRS597740SRS597737SRS597743SRS597730SRS597752SRS597753SRS565647SRS597748SRS597747SRS597755SRS565646SRS565648SRS565374SRS597751SRS6910408SRS6910420SRS6910386SRS6910390SRS6910396SRS6910421SRS6910422SRS6910388SRS6910391SRS6910419SRS6910389SRS6910397SRS6910394SRS6910392SRS6910424SRS6910387SRS6910385SRS6910423SRS6910393SRS6910395SRS629095SRS629340SRS629099SRS631191SRS629339SRS629097SRS629694SRS631192SRS631194SRS631208SRS629094SRS428710SRS629092SRS631190SRS631226SRS428704SRS631198SRS631223SRS631211SRS631216SRS631213SRS628362SRS631195SRS631218SRS631225SRS631224SRS428705SRS597765SRS597766SRS597768SRS597769SRS597762SRS597767SRS597761SRS597763SRS597770SRS597764SRS597758SRS597760SRS597759SRS597756SRS597757SRS597602SRS597608SRS597621SRS597625SRS597604SRS597617SRS597616SRS597622SRS597609SRS597614SRS597613SRS597624SRS597626SRS597597SRS597618SRS597611SRS597623SRS597601SRS597620SRS597598SRS597605SRS597595SRS597607SRS597610SRS614728SRS597615SRS597619SRS597612SRS597606SRS597603SRS428708SRS641741SRS428709SRS629338SRS641737SRS628373SRS628374SRS641736SRS631187SRS631188SRS629341SRS631196SRS629672SRS629671SRS631210SRS631215SRS631212SRS629678SRS631193SRS629692SRS629686SRS631230SRS629691SRS628370SRS628372SRS629321SRS628369SRS629334SRS628371SRS628376SRS631207SRS629687SRS597774SRS597788SRS597781SRS597809SRS597782SRS597811SRS597797SRS597808SRS597776SRS597778SRS597792SRS597812SRS597775SRS597780SRS597796SRS597785SRS597798SRS597795SRS597787SRS597791SRS597773SRS597777SRS597772SRS597786SRS597813SRS597794SRS597799SRS597789SRS597771SRS628363SRS631197SRS629683SRS628367SRS629693SRS629100SRS629679SRS629673SRS629326SRS629675SRS629681SRS629674SRS629676SRS631221SRS628366SRS628364SRS629669SRS628368SRS641742SRS629682SRS629325SRS629684SRS2165153SRS2165154SRS2165155SRS2165147SRS2165149SRS2165150SRS2165148SRS2165151SRS2165152SRS2165157SRS2165160SRS2165156SRS6910398SRS6910406SRS6910409SRS6910412SRS6910401SRS6910411SRS6910400SRS6910399SRS6910402SRS6910417SRS6910414SRS6910415SRS6910403SRS6910407SRS6910418SRS6910405SRS6910404SRS2165159SRS2165161SRS2165162SRS2165158SRS2165144SRS2165145SRS2165146SRS2165142SRS2165143SRS2165140SRS2165138SRS2165139SRS1512417SRS1512418SRS1512407SRS1512380SRS1512406SRS1512404SRS1512405SRS1512399SRS1496254SRS1496261SRS1338704SRS1496259SRS1496264SRS1496260SRS1496265SRS1496266SRS1496262SRS1496257SRS2505185SRS2505194SRS2505201SRS2505187SRS2505186SRS2505202SRS2505192

        cross-validation (CV) plot for ADMIXTURE analysis

        Note that the color-pattern is not consistent across the different values of K

        Bokeh Plot

        Fst-distance based NJ tree

        Fst distances were calculated using plink and NJ distances were calculated using Biopython module

        idx: 0 dist: 0.0423 support: 0.0000 height: 0.0000 name: Angusidx: 1 dist: 0.0102 support: 0.0000 height: 0.0321 name: Red_Angusidx: 2 dist: 0.0378 support: 0.0000 height: 0.0398 name: Maine_Anjouidx: 3 dist: 0.0332 support: 0.0000 height: 0.0468 name: Holsteinidx: 4 dist: 0.0340 support: 0.0000 height: 0.0459 name: Kholmogoryidx: 5 dist: 0.0850 support: 0.0000 height: 0.0002 name: Jerseyidx: 6 dist: 0.0724 support: 0.0000 height: 0.0127 name: Herefordidx: 7 dist: 0.0158 support: 0.0000 height: 0.0754 name: Charolaisidx: 8 dist: 0.0185 support: 0.0000 height: 0.0687 name: Gelbviehidx: 9 dist: 0.0277 support: 0.0000 height: 0.0595 name: Simmentalidx: 10 dist: 0.0030 support: 0.0000 height: 0.1058 name: Kazakh_Cattleidx: 11 dist: 0.0142 support: 0.0000 height: 0.1027 name: Mongolian_Cattleidx: 12 dist: 0.0586 support: 0.0000 height: 0.0529 name: Tibetan_Yellowidx: 13 dist: 0.0869 support: 0.0000 height: 0.0247 name: Yakutidx: 14 dist: 0.1132 support: 0.0000 height: 0.0403 name: Ndamaidx: 15 dist: 0.0433 support: 0.0000 height: 0.1498 name: Ankoleidx: 16 dist: 0.0000 support: 0.0000 height: 0.2898 name: Wenshan_Cattleidx: 17 dist: 0.0353 support: 0.0000 height: 0.0423 name: Inner2idx: 18 dist: 0.0075 support: 0.0000 height: 0.0776 name: Inner9idx: 19 dist: 0.0052 support: 0.0000 height: 0.0799 name: Inner10idx: 20 dist: 0.0017 support: 0.0000 height: 0.0851 name: Inner13idx: 21 dist: 0.0017 support: 0.0000 height: 0.0851 name: Inner15idx: 22 dist: 0.0044 support: 0.0000 height: 0.0868 name: Inner14idx: 23 dist: 0.0019 support: 0.0000 height: 0.0912 name: Inner12idx: 24 dist: 0.0060 support: 0.0000 height: 0.0872 name: Inner8idx: 25 dist: 0.0157 support: 0.0000 height: 0.0931 name: Inner11idx: 26 dist: 0.0081 support: 0.0000 height: 0.1089 name: Inner7idx: 27 dist: 0.0040 support: 0.0000 height: 0.1169 name: Inner6idx: 28 dist: 0.0093 support: 0.0000 height: 0.1116 name: Inner4idx: 29 dist: 0.0326 support: 0.0000 height: 0.1209 name: Inner5idx: 30 dist: 0.0396 support: 0.0000 height: 0.1535 name: Inner3idx: 31 dist: 0.0967 support: 0.0000 height: 0.1931 name: Inner1idx: 32 dist: 0.0000 support: 0.0000 height: 0.2898 name: 32AngusRed_AngusMaine_AnjouHolsteinKholmogoryJerseyHerefordCharolaisGelbviehSimmentalKazakh_CattleMongolian_CattleTibetan_YellowYakutNdamaAnkoleWenshan_Cattle

        Principal Component Analysis (PCA)

        PCA was carried out using smartpca program of eigensoft package

        Bokeh Plot

        Q-matrices of ADMIXTURE analysis

        Note that the color-pattern is not consistent across the different values of K

        Bokeh Plot

        Treemix_p

        Treemix_results.

        Treemix

        OptM results

        Treemix_m1

        Treemix_m2

        Treemix_m3

        Treemix_m4

        Treemix_m5

        Treemix_m6

        Treemix_m7

        Treemix_m8

        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.