BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525270.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,520,368 number of mapped reads = 1,331,913 (87.6%) number of supplementary alignments = 4,682 (0.31%) number of secondary alignments = 0 number of mapped bases = 76,977,671 bp number of sequenced bases = 76,951,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,097 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2672 >>>>>>> ACTG content number of A's = 18,106,810 bp (23.53%) number of C's = 14,178,664 bp (18.43%) number of T's = 24,969,121 bp (32.45%) number of G's = 19,695,259 bp (25.59%) number of N's = 1,498 bp (0%) GC percentage = 44.02% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 401,979 number of insertions = 5,184 mapped reads with insertion percentage = 0.39% number of deletions = 16,486 mapped reads with deletion percentage = 1.23% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2446X There is a 2.27% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6444485 0.02585544210138598 0.3826887324396134 chr2 243199373 6097773 0.02507314441143728 0.3380127032833791 chr3 198022430 4425570 0.022348831897477474 0.16122222888460114 chr4 191154276 4742358 0.02480906050984703 0.19566993576887126 chr5 180915260 4410775 0.024380336959966782 0.16717530397198455 chr6 171115067 4098602 0.023952315081640356 0.19552230433203763 chr7 159138663 4396572 0.027627302612187963 0.31694057101374007 chr8 146364022 4075872 0.027847499298700607 0.31325737300840495 chr9 141213431 2583444 0.018294605418942057 0.17275044979338997 chr10 135534747 3438381 0.025369000024768558 0.25253182839910404 chr11 135006516 2737275 0.020275132498049204 0.18834967495456917 chr12 133851895 3789557 0.028311567796630747 0.1817422835076863 chr13 115169878 2341760 0.02033309438775302 0.15577192538987983 chr14 107349540 2571784 0.023957103123124702 0.16891700535764786 chr15 102531392 2805142 0.027358860006504154 0.18002307309629073 chr16 90354753 2589998 0.028664767640945242 0.18906750222449387 chr17 81195210 3269352 0.04026533092284631 0.2235195268153736 chr18 78077248 1445924 0.018519146576477696 0.2736115232610149 chr19 59128983 1904847 0.03221511521684721 0.29944865065466647 chr20 63025520 2499412 0.039657142059280115 0.22045948232992837 chr21 48129895 987978 0.020527325064806395 0.1741307997584301 chr22 51304566 703587 0.01371392557925546 0.125408811306689 chrMT 16571 204255 12.326051535815582 7.918570029349929 chrX 155270560 4123043 0.02655392625620723 0.1885751686302545 chrY 59373566 289925 0.004883065302158203 0.19785305578843382