BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505952.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,381,008 number of mapped reads = 4,556,865 (71.41%) number of supplementary alignments = 280 (0%) number of secondary alignments = 0 number of mapped bases = 211,386,825 bp number of sequenced bases = 211,344,077 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,386 duplication rate = 5.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4607 >>>>>>> ACTG content number of A's = 62,093,122 bp (29.38%) number of C's = 44,129,779 bp (20.88%) number of T's = 60,791,322 bp (28.76%) number of G's = 44,329,187 bp (20.97%) number of N's = 667 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,069,037 number of insertions = 9,308 mapped reads with insertion percentage = 0.2% number of deletions = 30,947 mapped reads with deletion percentage = 0.68% homopolymer indels = 45.6% >>>>>>> Coverage mean coverageData = 0.0683X std coverageData = 0.639X There is a 5.08% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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% 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 23553994 0.09449923898083287 1.356399494564546 chr2 243199373 13725041 0.05643534697764208 0.45737184098683487 chr3 198022430 13962977 0.07051209804869074 0.3418686073930375 chr4 191154276 9558095 0.050001994200747045 0.2964704337212196 chr5 180915260 12769783 0.07058433323977203 0.3455283275546135 chr6 171115067 15452355 0.09030388305899445 0.49066078011076697 chr7 159138663 12738686 0.08004771285529777 1.128820936441849 chr8 146364022 13329657 0.09107195072843789 0.8826247171703088 chr9 141213431 6112180 0.04328327664526471 0.3946954623304604 chr10 135534747 7374983 0.05441396515094391 0.5695529781574428 chr11 135006516 10511658 0.07786037527255352 0.6098350226485503 chr12 133851895 6637245 0.04958648512223155 0.3050890124815939 chr13 115169878 6265848 0.05440526732172105 0.29405977259134364 chr14 107349540 8223912 0.07660873069414177 0.36635030914079986 chr15 102531392 4529563 0.04417732863706756 0.26378465187260797 chr16 90354753 7793984 0.08625981192157096 0.4095816101551284 chr17 81195210 4009826 0.04938500682490999 0.33347643692049544 chr18 78077248 5672905 0.0726575941815982 0.7310082317621162 chr19 59128983 5854775 0.0990170082918558 1.0078308241148473 chr20 63025520 5668960 0.08994705636700816 0.39393996562552497 chr21 48129895 3461352 0.0719168824282704 0.37873217650615615 chr22 51304566 1822759 0.035528202304644776 0.2374792407031551 chrMT 16571 22164 1.3375173495866273 1.7210341583494384 chrX 155270560 11720961 0.07548733642745926 0.4143155112683929 chrY 59373566 613162 0.01032718836527353 0.1666096104679207