BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053632.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,193,445 number of mapped reads = 10,246,402 (77.66%) number of supplementary alignments = 273 (0%) number of secondary alignments = 0 number of mapped bases = 485,002,007 bp number of sequenced bases = 484,910,561 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,590,985 duplication rate = 17.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6 >>>>>>> ACTG content number of A's = 141,924,739 bp (29.27%) number of C's = 93,812,451 bp (19.35%) number of T's = 143,479,603 bp (29.59%) number of G's = 105,687,628 bp (21.8%) number of N's = 6,140 bp (0%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 2,493,192 number of insertions = 18,860 mapped reads with insertion percentage = 0.18% number of deletions = 61,773 mapped reads with deletion percentage = 0.6% homopolymer indels = 48.03% >>>>>>> Coverage mean coverageData = 0.1567X std coverageData = 1.1413X There is a 6.05% of reference with a coverageData >= 1X There is a 2.78% of reference with a coverageData >= 2X There is a 1.7% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.81% of reference with a coverageData >= 5X There is a 0.59% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 38535517 0.15460550046132082 1.1769207404405337 chr2 243199373 41044741 0.16876992935339516 1.350512012363099 chr3 198022430 32966181 0.16647700465043277 1.0558393618686142 chr4 191154276 31125047 0.1628268414984345 1.1015587478721327 chr5 180915260 29754825 0.1644682985835468 1.0590799789698584 chr6 171115067 28250272 0.16509517540030533 1.1331719579946953 chr7 159138663 26045136 0.16366315707955897 1.3702423424657435 chr8 146364022 24390923 0.16664561868899722 1.1449029290407575 chr9 141213431 19843102 0.1405185176755602 1.103140463053208 chr10 135534747 22566042 0.16649635978587837 1.1784005585103985 chr11 135006516 22328093 0.16538529888438866 1.2107288202963558 chr12 133851895 22466499 0.1678459539179479 1.0892570541437512 chr13 115169878 15656955 0.1359466144437524 0.975757472502632 chr14 107349540 14929615 0.13907479249561758 1.1161938411079602 chr15 102531392 14171616 0.1382173373789756 0.9839309523965066 chr16 90354753 13962472 0.15452946896993897 1.0323927671951343 chr17 81195210 12983511 0.15990488847802722 1.066806874316028 chr18 78077248 12574062 0.161046429300377 1.2300552167539327 chr19 59128983 8953123 0.1514168271759384 1.169802967195949 chr20 63025520 10512722 0.16680103551704134 1.1215241954812403 chr21 48129895 6237363 0.12959436125925478 1.0601908356566292 chr22 51304566 5317960 0.10365471174631903 0.8115525705277532 chrMT 16571 93237 5.6265162030052505 10.278576418397009 chrX 155270560 29107807 0.18746507386847835 1.2693629058633897 chrY 59373566 1185186 0.019961509470392935 0.3925601201488245