BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238041.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 = 2,168,087 number of mapped reads = 1,922,656 (88.68%) number of supplementary alignments = 15,166 (0.7%) number of secondary alignments = 0 number of mapped bases = 124,967,090 bp number of sequenced bases = 124,896,236 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,019 duplication rate = 3.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.906 >>>>>>> ACTG content number of A's = 34,551,021 bp (27.66%) number of C's = 22,692,327 bp (18.17%) number of T's = 39,579,440 bp (31.69%) number of G's = 27,814,464 bp (22.27%) number of N's = 258,984 bp (0.21%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,139,394 number of insertions = 9,752 mapped reads with insertion percentage = 0.5% number of deletions = 43,051 mapped reads with deletion percentage = 2.21% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 0.0404X std coverageData = 0.3786X There is a 3.44% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 9457212 0.037942581495112905 0.7630000552060097 chr2 243199373 13040011 0.05361860451835951 0.4616408388935965 chr3 198022430 5360754 0.027071448421272275 0.1868533573672885 chr4 191154276 6902085 0.03610740572708925 0.23991544635513018 chr5 180915260 10339464 0.05715086720711122 0.2734492581919507 chr6 171115067 10125840 0.05917561894184339 0.34402096283300826 chr7 159138663 7317170 0.0459798383501563 0.538066887507612 chr8 146364022 7335171 0.050115943110664175 0.44024095489792736 chr9 141213431 5537144 0.039211171067715225 0.31515054174651097 chr10 135534747 5942082 0.04384176110942237 0.3484554817492727 chr11 135006516 4598644 0.034062385551820326 0.2564339752179203 chr12 133851895 5873994 0.04388427971079528 0.24373747633797468 chr13 115169878 2438382 0.021172046392199877 0.16629059851426153 chr14 107349540 3750525 0.03493750415698102 0.2298542555869718 chr15 102531392 2832527 0.027625948938643105 0.19422999035698843 chr16 90354753 2180987 0.024138043961007785 0.196872116432102 chr17 81195210 2858170 0.035201214455877386 0.22511679845963287 chr18 78077248 3228989 0.041356337252050686 0.4987157387555788 chr19 59128983 1807776 0.03057343299816268 0.4411704241992226 chr20 63025520 2884183 0.04576214523894448 0.2476424298754645 chr21 48129895 1722836 0.03579554869172268 0.23686365483893904 chr22 51304566 720125 0.014036275055908279 0.13218739222494988 chrMT 16571 66228 3.996620602256955 2.8595614645546314 chrX 155270560 8325318 0.05361813598147646 0.28443501064234156 chrY 59373566 321473 0.005414412871883087 0.13748416138876302