BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013274.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,334,117 number of mapped reads = 1,111,936 (83.35%) number of supplementary alignments = 15,314 (1.15%) number of secondary alignments = 0 number of mapped bases = 71,391,262 bp number of sequenced bases = 71,323,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,076 duplication rate = 5.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5092 >>>>>>> ACTG content number of A's = 20,353,629 bp (28.54%) number of C's = 12,460,796 bp (17.47%) number of T's = 23,515,137 bp (32.97%) number of G's = 14,977,793 bp (21%) number of N's = 16,431 bp (0.02%) GC percentage = 38.47% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 722,856 number of insertions = 5,615 mapped reads with insertion percentage = 0.5% number of deletions = 38,658 mapped reads with deletion percentage = 3.41% homopolymer indels = 42.1% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.2997X There is a 1.68% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3920349 0.01572854255797421 0.5443846427761697 chr2 243199373 7027795 0.02889725788890089 0.29416480215232876 chr3 198022430 3297511 0.016652209550200955 0.16632242053243343 chr4 191154276 5685927 0.029745225265062864 0.23678176331660591 chr5 180915260 4824402 0.026666639397914804 0.2176116017889686 chr6 171115067 1719788 0.010050476735634273 0.14172662090526952 chr7 159138663 5578322 0.03505321645186877 0.3018319492104954 chr8 146364022 5977939 0.04084295387837866 0.6321019473371098 chr9 141213431 2832825 0.020060591828549225 0.2287058419809743 chr10 135534747 3986386 0.029412280527590463 0.29130405105621415 chr11 135006516 1808237 0.013393701678813784 0.16480468882561763 chr12 133851895 5278343 0.039434204498935185 0.2648768574804948 chr13 115169878 705836 0.006128651104414646 0.09898260374066638 chr14 107349540 3765218 0.035074374794712676 0.2520110872034379 chr15 102531392 1403840 0.013691806700527385 0.14788415923680087 chr16 90354753 1217308 0.013472539734572679 0.16329370269030577 chr17 81195210 1272820 0.01567604788509076 0.16108112588483905 chr18 78077248 2603941 0.033350829680882196 0.43152354432418044 chr19 59128983 1489354 0.02518822283819764 0.3528456606619571 chr20 63025520 1449116 0.022992527471411582 0.20648663446899 chr21 48129895 1575726 0.03273902841466826 0.24287719525156518 chr22 51304566 468542 0.009132559468488633 0.11902438206596075 chrMT 16571 11761 0.7097338724277352 1.0157398721205861 chrX 155270560 3293030 0.021208334664343326 0.2000915500590002 chrY 59373566 196946 0.003317065375524185 0.10397890647506779