BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536761.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 21,326,306 number of mapped reads = 20,834,384 (97.69%) number of supplementary alignments = 542 (0%) number of secondary alignments = 0 number of mapped bases = 1,039,143,287 bp number of sequenced bases = 1,039,052,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 221,277 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6583 >>>>>>> ACTG content number of A's = 320,356,004 bp (30.83%) number of C's = 197,081,572 bp (18.97%) number of T's = 320,639,173 bp (30.86%) number of G's = 200,938,934 bp (19.34%) number of N's = 36,673 bp (0%) GC percentage = 38.31% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 2,033,084 number of insertions = 61,038 mapped reads with insertion percentage = 0.29% number of deletions = 55,181 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.34% >>>>>>> Coverage mean coverageData = 0.3357X std coverageData = 0.6677X There is a 25.26% of reference with a coverageData >= 1X There is a 6.27% of reference with a coverageData >= 2X There is a 1.52% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% 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 78984474 0.31688777216727576 0.6616632721553543 chr2 243199373 94019069 0.38659256329579433 0.7047638875524251 chr3 198022430 86718745 0.4379238503436202 0.7544233660494227 chr4 191154276 82172571 0.4298756623158145 0.7388423963234875 chr5 180915260 71497291 0.3951976798419326 0.7102763531898154 chr6 171115067 73947521 0.43215084619053445 0.7518314613079691 chr7 159138663 58177858 0.3655796580369662 0.6930269431031313 chr8 146364022 56119736 0.3834257574583459 0.6981687987307275 chr9 141213431 42806945 0.30313649839723816 0.6428599885595658 chr10 135534747 44605175 0.32910508919162995 0.6476045985679908 chr11 135006516 48712654 0.3608170586373772 0.6963903412994081 chr12 133851895 47788595 0.35702591285689306 0.6861721788887657 chr13 115169878 39609865 0.34392556185567896 0.6755620078704858 chr14 107349540 32412134 0.3019308140491333 0.6370952912501543 chr15 102531392 27810320 0.2712371251138383 0.6088844634359015 chr16 90354753 19553654 0.21640979971468685 0.5327218371808408 chr17 81195210 17786354 0.21905669065946132 0.534563409009842 chr18 78077248 30384695 0.38916196175357 0.7062877807874801 chr19 59128983 8939676 0.15118940909232279 0.4371110889142568 chr20 63025520 16921740 0.2684902877437584 0.596284265366841 chr21 48129895 12937201 0.26879761528671525 0.6146514716063864 chr22 51304566 5798073 0.11301280669638644 0.38350627383513025 chrMT 16571 797 0.04809607145012371 0.22895620120612836 chrX 155270560 36371641 0.2342468591599077 0.5361951220763534 chrY 59373566 5066503 0.0853326377600429 0.339644557957551