BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505917.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 = 7,683,568 number of mapped reads = 5,248,577 (68.31%) number of supplementary alignments = 315 (0%) number of secondary alignments = 0 number of mapped bases = 240,471,031 bp number of sequenced bases = 240,423,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 304,512 duplication rate = 4.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1638 >>>>>>> ACTG content number of A's = 69,865,837 bp (29.06%) number of C's = 50,868,320 bp (21.16%) number of T's = 68,295,893 bp (28.41%) number of G's = 51,392,888 bp (21.38%) number of N's = 666 bp (0%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,213,485 number of insertions = 10,691 mapped reads with insertion percentage = 0.2% number of deletions = 34,228 mapped reads with deletion percentage = 0.65% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0777X std coverageData = 0.6253X There is a 5.95% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.32% 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% 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 25938342 0.10406530541803545 1.3618137516360624 chr2 243199373 15521964 0.06382402967790546 0.4259896763187137 chr3 198022430 15415483 0.07784715600146913 0.35127094498327965 chr4 191154276 10538560 0.0551311758257503 0.2942446497338473 chr5 180915260 14471247 0.0799890899197779 0.35919815720444825 chr6 171115067 17300566 0.10110486646976563 0.5313076308934348 chr7 159138663 16296531 0.10240459918907324 0.8869358697200991 chr8 146364022 15036274 0.10273203615571591 0.924985849906511 chr9 141213431 7230733 0.05120428665174207 0.35584759403936467 chr10 135534747 7497761 0.05531984355273854 0.6117724496442946 chr11 135006516 12996106 0.09626280556710315 0.607826496692717 chr12 133851895 6771166 0.050587001401810563 0.29257488228185285 chr13 115169878 6985135 0.06065071111736352 0.30474535312323836 chr14 107349540 8852450 0.08246379071582421 0.45369870802963497 chr15 102531392 4656450 0.0454148715741614 0.26011575527330233 chr16 90354753 8613812 0.09533324716188422 0.43468941845320924 chr17 81195210 4300667 0.05296700384172909 0.3291777154757881 chr18 78077248 6139937 0.07863925992883355 0.7256272834885807 chr19 59128983 6659317 0.11262356736289546 0.9095618475452539 chr20 63025520 6543532 0.1038235305317592 0.4121584842917209 chr21 48129895 3844997 0.07988791581614711 0.3728804987175024 chr22 51304566 1807196 0.03522485698446411 0.23151422463155522 chrMT 16571 13703 0.826926558445477 1.1374723796927588 chrX 155270560 16351270 0.10530824388087477 0.45273309176494336 chrY 59373566 687832 0.011584818739032788 0.16117138568826644