BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525200.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,271,906 number of mapped reads = 1,166,892 (91.74%) number of supplementary alignments = 4,001 (0.31%) number of secondary alignments = 0 number of mapped bases = 69,566,040 bp number of sequenced bases = 69,542,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,955 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0288 >>>>>>> ACTG content number of A's = 17,915,177 bp (25.76%) number of C's = 14,212,661 bp (20.44%) number of T's = 22,060,050 bp (31.72%) number of G's = 15,352,926 bp (22.08%) number of N's = 1,696 bp (0%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 345,352 number of insertions = 5,683 mapped reads with insertion percentage = 0.49% number of deletions = 14,762 mapped reads with deletion percentage = 1.26% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.2263X There is a 2.08% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6986576 0.028030325348717987 0.3395278261769769 chr2 243199373 5316383 0.021860183825391687 0.2645713205783248 chr3 198022430 7353871 0.03713655569220113 0.20451181514861247 chr4 191154276 2848050 0.014899222029435532 0.13716707955239818 chr5 180915260 2856121 0.01578706517073242 0.13251285970766566 chr6 171115067 4057960 0.023714802390837973 0.17511227201137797 chr7 159138663 4739688 0.0297833845694682 0.4030435852293539 chr8 146364022 4140825 0.028291276390314007 0.23232443181192447 chr9 141213431 2502229 0.017719483070983526 0.17694062512659467 chr10 135534747 3451628 0.02546673879872296 0.25452614364495174 chr11 135006516 2856987 0.021161845254935696 0.210427329995088 chr12 133851895 2823591 0.02109488999016413 0.1554118155658382 chr13 115169878 1977142 0.017167179772474884 0.13770168935536234 chr14 107349540 4495598 0.041878130078619805 0.21853164181582058 chr15 102531392 1678631 0.016371873698935054 0.1374471335682075 chr16 90354753 1716365 0.01899584629488169 0.1612706498823231 chr17 81195210 1241248 0.015287207213331919 0.13339802236148368 chr18 78077248 1381046 0.01768820028082957 0.36587858594177364 chr19 59128983 792598 0.013404559993869672 0.2523048179498806 chr20 63025520 1157513 0.01836578262265825 0.14510629824101245 chr21 48129895 816936 0.016973567052244763 0.14588737872934962 chr22 51304566 533791 0.010404356602490313 0.10719142783682721 chrMT 16571 80951 4.885100476736468 3.438889737909655 chrX 155270560 3555249 0.022897122287702187 0.17119024844632122 chrY 59373566 205063 0.0034537760457237824 0.11783146233472676