BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231754.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 = 4,748,558 number of mapped reads = 4,472,564 (94.19%) number of supplementary alignments = 20,789 (0.44%) number of secondary alignments = 0 number of mapped bases = 301,622,740 bp number of sequenced bases = 301,513,429 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 339,117 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0874 >>>>>>> ACTG content number of A's = 78,821,649 bp (26.14%) number of C's = 58,324,207 bp (19.34%) number of T's = 86,284,127 bp (28.62%) number of G's = 78,018,637 bp (25.88%) number of N's = 64,809 bp (0.02%) GC percentage = 45.22% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,043,285 number of insertions = 21,597 mapped reads with insertion percentage = 0.48% number of deletions = 66,613 mapped reads with deletion percentage = 1.47% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.0974X std coverageData = 18.526X There is a 7.04% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 34789800 0.13957758604741852 1.3924835727039024 chr2 243199373 29285321 0.12041692640383575 66.03987721184038 chr3 198022430 18383453 0.09283520558756904 0.38746598886759104 chr4 191154276 20993767 0.10982630072057609 0.47189237989648497 chr5 180915260 19624943 0.10847588533990997 0.4410415400335588 chr6 171115067 19929797 0.1164701469567259 0.685304306677398 chr7 159138663 13883040 0.08723863665990457 1.2215544777389087 chr8 146364022 15377095 0.10506062070363166 0.769557192941116 chr9 141213431 7749057 0.05487478737061491 0.8942132166001193 chr10 135534747 9321654 0.0687768576422694 0.5687634069450473 chr11 135006516 10773229 0.07979784472032446 0.9127957700210145 chr12 133851895 9578383 0.07155956215636693 0.36086154631142914 chr13 115169878 8717339 0.07569113687868975 0.3448640700689406 chr14 107349540 12793937 0.11918017534122642 0.6563093499330951 chr15 102531392 5230466 0.051013313073912034 0.2903266367719507 chr16 90354753 10911126 0.12075873861334113 0.6090734215583724 chr17 81195210 6067698 0.07472975314676814 0.5059608816501664 chr18 78077248 8787992 0.11255509415495792 1.8002683306748577 chr19 59128983 10343372 0.17492896842145925 1.1644711709121938 chr20 63025520 7362859 0.11682345500679725 0.4740067130481358 chr21 48129895 6313073 0.13116739606433797 0.5683522873537483 chr22 51304566 2847688 0.05550554701115686 0.3011356244940109 chrMT 16571 7597 0.45845151167702614 1.179491082929252 chrX 155270560 11860168 0.07638388114269698 0.5783468302498984 chrY 59373566 689886 0.011619413258755588 0.22007126908435298