BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971301.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,308,239 number of mapped reads = 8,744,770 (84.83%) number of secondary alignments = 0 number of mapped bases = 345,016,576 bp number of sequenced bases = 344,982,919 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 590,626 duplication rate = 5.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9549 >>>>>>> ACTG content number of A's = 99,114,034 bp (28.73%) number of C's = 70,171,129 bp (20.34%) number of T's = 102,605,981 bp (29.74%) number of G's = 73,089,223 bp (21.19%) number of N's = 2,552 bp (0%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 938,060 number of insertions = 11,425 mapped reads with insertion percentage = 0.13% number of deletions = 26,681 mapped reads with deletion percentage = 0.3% homopolymer indels = 40.36% >>>>>>> Coverage mean coverageData = 0.1115X std coverageData = 0.9031X There is a 8.74% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 30577778 0.12267884379714344 1.9378760860717015 chr2 243199373 28884013 0.11876680701804276 0.6992814300661302 chr3 198022430 24548938 0.12397049162562039 0.4322299938137935 chr4 191154276 23346782 0.1221358082515507 0.45469685283166517 chr5 180915260 22043273 0.1218430827780918 0.4446412503119883 chr6 171115067 20230866 0.11822960043606212 0.5329923905889002 chr7 159138663 19186094 0.12056211632241752 1.1754583478905996 chr8 146364022 18424311 0.12588005404770852 1.6173566234037493 chr9 141213431 14702744 0.10411717848566401 0.7238540910577912 chr10 135534747 16371664 0.12079311292771291 0.8002454315170623 chr11 135006516 16255636 0.12040630690743845 0.7168989480272788 chr12 133851895 16123711 0.12045934052708032 0.4425879552419341 chr13 115169878 11813274 0.10257260149220615 0.3834280040400708 chr14 107349540 10775942 0.1003818181242323 0.48498515800208125 chr15 102531392 9467861 0.09234109491071768 0.367480749575549 chr16 90354753 9007816 0.09969388107341735 0.4592570508558647 chr17 81195210 8267880 0.10182718906694127 0.45674527373471996 chr18 78077248 8984042 0.11506606892701957 1.311082750050485 chr19 59128983 5926142 0.10022397983743438 1.5835341011618949 chr20 63025520 6651992 0.1055444207362351 0.43697302764307094 chr21 48129895 4410865 0.09164501605499036 0.4561111175487114 chr22 51304566 3285090 0.06403114295908867 0.3884533444631556 chrMT 16571 49493 2.9867237945808944 3.428335365171939 chrX 155270560 12517337 0.08061629326254764 0.45711215189230714 chrY 59373566 3163032 0.05327340453157218 0.4483632864467108