BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708594.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,651,782 number of mapped reads = 4,525,805 (97.29%) number of supplementary alignments = 141 (0%) number of secondary alignments = 0 number of mapped bases = 225,745,754 bp number of sequenced bases = 225,726,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,101 duplication rate = 0.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7105 >>>>>>> ACTG content number of A's = 69,833,140 bp (30.94%) number of C's = 42,914,305 bp (19.01%) number of T's = 69,552,352 bp (30.81%) number of G's = 43,420,232 bp (19.24%) number of N's = 6,018 bp (0%) GC percentage = 38.25% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 330,770 number of insertions = 14,206 mapped reads with insertion percentage = 0.31% number of deletions = 11,505 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.96% >>>>>>> Coverage mean coverageData = 0.0729X std coverageData = 0.281X There is a 6.78% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.03% 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 17077464 0.06851523150267297 0.27337860162383165 chr2 243199373 20376606 0.08378560252291439 0.30452640745600834 chr3 198022430 17449288 0.08811773494548067 0.3071388442119487 chr4 191154276 17527610 0.09169352821592126 0.31300453186601973 chr5 180915260 15637288 0.08643432289791364 0.3042859428512567 chr6 171115067 14671902 0.08574289954256337 0.30262602977716807 chr7 159138663 12691631 0.07975202732474886 0.29318657740078613 chr8 146364022 12566451 0.08585751353566931 0.3032343508816149 chr9 141213431 9199676 0.0651473159093486 0.26524993636947525 chr10 135534747 9414967 0.06946533791810597 0.2726245860474081 chr11 135006516 10405599 0.07707479096786707 0.28915577368099615 chr12 133851895 10137605 0.07573747835247308 0.2853108708154951 chr13 115169878 8561862 0.07434115715569309 0.2834874109639591 chr14 107349540 6987759 0.06509351600388787 0.26545124693584027 chr15 102531392 6011506 0.05863088253010356 0.25237870623269254 chr16 90354753 4052154 0.04484715928557737 0.2195168858105008 chr17 81195210 3664999 0.045138118369297896 0.22048994670509878 chr18 78077248 6624067 0.08483991392729416 0.30103781972623084 chr19 59128983 1847408 0.03124369651343403 0.18208429268296586 chr20 63025520 3408877 0.054087249101633754 0.2407180885459183 chr21 48129895 2937014 0.061022655461849644 0.2589589768159096 chr22 51304566 1296913 0.025278705213099356 0.1643081681916979 chrMT 16571 137 0.00826745519280671 0.09054890599803868 chrX 155270560 12864283 0.08285075419319671 0.29878129269766524 chrY 59373566 332688 0.005603301644371504 0.07846637652066579