BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236066.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 = 1,391,944 number of mapped reads = 1,236,912 (88.86%) number of supplementary alignments = 9,457 (0.68%) number of secondary alignments = 0 number of mapped bases = 82,649,768 bp number of sequenced bases = 82,603,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,932 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1613 >>>>>>> ACTG content number of A's = 23,309,405 bp (28.22%) number of C's = 14,590,778 bp (17.66%) number of T's = 26,885,273 bp (32.55%) number of G's = 17,780,893 bp (21.53%) number of N's = 37,272 bp (0.05%) GC percentage = 39.19% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 682,760 number of insertions = 6,203 mapped reads with insertion percentage = 0.5% number of deletions = 26,473 mapped reads with deletion percentage = 2.11% homopolymer indels = 46.05% >>>>>>> Coverage mean coverageData = 0.0267X std coverageData = 0.2793X There is a 2.32% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6573455 0.026372873109110528 0.3727535509249433 chr2 243199373 5556695 0.02284831137290802 0.30335174107959445 chr3 198022430 8524014 0.04304569941900016 0.23111015158396112 chr4 191154276 3189525 0.016685606342387027 0.1550108026527037 chr5 180915260 4156340 0.0229739602950022 0.16911756958651886 chr6 171115067 8734831 0.05104653350017389 0.3536070291133595 chr7 159138663 4843590 0.03043628687517627 0.34798605737903526 chr8 146364022 5189063 0.03545313205454275 0.5720292530303606 chr9 141213431 3257082 0.023064959026454078 0.2628607141001513 chr10 135534747 3393813 0.02504016921948436 0.259449083016491 chr11 135006516 1681386 0.012454109992735461 0.1689212926664898 chr12 133851895 3512318 0.02624033077753587 0.18525980657820323 chr13 115169878 2649330 0.02300367115088895 0.1682063870533116 chr14 107349540 3218459 0.029981115894860844 0.1968056472480505 chr15 102531392 2208542 0.021540154258317297 0.165342805021456 chr16 90354753 2133741 0.02361514949855488 0.18662031028363005 chr17 81195210 2081797 0.025639406561052062 0.2014167171058959 chr18 78077248 2421136 0.03100949459694071 0.4339244192297443 chr19 59128983 1325982 0.022425246177496406 0.2992766986548684 chr20 63025520 1518120 0.0240873855542961 0.17506425578784607 chr21 48129895 2061292 0.04282768537101525 0.2411711730096484 chr22 51304566 825524 0.01609065360771203 0.13895011086859183 chrMT 16571 23484 1.4171745821012613 1.4230348239195154 chrX 155270560 3357247 0.021621915963979263 0.17909872428283177 chrY 59373566 213002 0.003587488748780897 0.09824121645130612