BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237836.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,523,187 number of mapped reads = 1,084,197 (71.18%) number of supplementary alignments = 5,348 (0.35%) number of secondary alignments = 0 number of mapped bases = 69,535,779 bp number of sequenced bases = 69,492,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,687 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6227 >>>>>>> ACTG content number of A's = 20,353,644 bp (29.29%) number of C's = 11,751,013 bp (16.91%) number of T's = 21,462,970 bp (30.89%) number of G's = 15,864,998 bp (22.83%) number of N's = 59,768 bp (0.09%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 750,736 number of insertions = 6,287 mapped reads with insertion percentage = 0.57% number of deletions = 27,365 mapped reads with deletion percentage = 2.48% homopolymer indels = 48.74% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.2058X There is a 1.98% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.02% 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 5866809 0.02353779090484192 0.26973664119346763 chr2 243199373 6345679 0.026092497368403987 0.23232009756077138 chr3 198022430 5069437 0.025600317095391668 0.18799021204829033 chr4 191154276 4486399 0.023470042595332787 0.17813705747022135 chr5 180915260 4207026 0.023254124610604988 0.1735732000841425 chr6 171115067 3889549 0.022730605014460826 0.18338932382013295 chr7 159138663 4041343 0.025395104645311743 0.2556639435712621 chr8 146364022 3737956 0.02553876252457725 0.26553511756865605 chr9 141213431 2772549 0.01963374857735735 0.19334937410633002 chr10 135534747 3080225 0.02272645995347599 0.2055766137205971 chr11 135006516 2924506 0.021661961856715123 0.20678323555806663 chr12 133851895 3581756 0.026759098180866248 0.19459390740280458 chr13 115169878 2553898 0.022175051709267243 0.17370836194878617 chr14 107349540 2011188 0.018734947536803603 0.16181923459791214 chr15 102531392 1919071 0.018716911597181866 0.1591729889370718 chr16 90354753 1648040 0.01823966028660385 0.16658424450859263 chr17 81195210 1412746 0.01739937614546474 0.15703370804762384 chr18 78077248 1737850 0.022258084711182444 0.3019013522740512 chr19 59128983 1019369 0.017239751950409835 0.1913466128117214 chr20 63025520 1345939 0.021355460454749123 0.16932381849665698 chr21 48129895 952674 0.019793810063371216 0.1683261950221919 chr22 51304566 572727 0.011163275409054235 0.1213437924231522 chrMT 16571 36527 2.204272524289421 2.250636526495925 chrX 155270560 4126680 0.026577349885258353 0.19292705066613794 chrY 59373566 195836 0.0032983701871637625 0.0785581328692404