BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548977.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,332,845 number of mapped reads = 4,563,820 (44.17%) number of secondary alignments = 0 number of mapped bases = 180,450,255 bp number of sequenced bases = 180,426,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,502 duplication rate = 2.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1123 >>>>>>> ACTG content number of A's = 56,007,621 bp (31.04%) number of C's = 33,542,274 bp (18.59%) number of T's = 56,703,406 bp (31.43%) number of G's = 34,163,438 bp (18.93%) number of N's = 9,832 bp (0.01%) GC percentage = 37.53% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 555,842 number of insertions = 6,952 mapped reads with insertion percentage = 0.15% number of deletions = 18,848 mapped reads with deletion percentage = 0.41% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0583X std coverageData = 0.4192X There is a 4.88% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14306010 0.05739608568517869 0.735586464666538 chr2 243199373 15719464 0.06463612058736681 0.37894692918655964 chr3 198022430 12941485 0.06535363190927411 0.29686423649921234 chr4 191154276 13033769 0.06818455371618264 0.309447287143781 chr5 180915260 11948278 0.0660435056722136 0.30401693604811836 chr6 171115067 11303080 0.06605543391453658 0.3551963780067598 chr7 159138663 10304776 0.06475344084045748 0.6353095164327035 chr8 146364022 9670873 0.06607411348671466 0.5209969529387609 chr9 141213431 7755418 0.05491983266095985 0.3648179904142621 chr10 135534747 8516528 0.06283649166364697 0.368349574370648 chr11 135006516 8406939 0.06227061662712635 0.3853660999488154 chr12 133851895 8296014 0.061979055283453405 0.3012072416807953 chr13 115169878 6293194 0.054642707878877844 0.2695987784585267 chr14 107349540 5706567 0.05315874665135966 0.3283663927279956 chr15 102531392 5118512 0.049921413336512586 0.25690109357283447 chr16 90354753 4523961 0.050068876841487246 0.27296669542696816 chr17 81195210 4114414 0.05067311236709653 0.27929905280369505 chr18 78077248 5036015 0.06450041630565667 0.6002665476920845 chr19 59128983 2808611 0.04749973460561634 0.7255641976287132 chr20 63025520 3438610 0.054559010381826284 0.28013981346240213 chr21 48129895 2352468 0.04887748041004453 0.2834575445158457 chr22 51304566 969047 0.018888123914740845 0.1784187550780416 chrMT 16571 2789 0.16830607688129864 0.4686110762884476 chrX 155270560 6354586 0.04092589090939068 0.28100304866601256 chrY 59373566 1528847 0.025749623999340044 0.2824262491277528