BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240205.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 = 2,177,998 number of mapped reads = 1,770,584 (81.29%) number of supplementary alignments = 8,615 (0.4%) number of secondary alignments = 0 number of mapped bases = 110,017,803 bp number of sequenced bases = 109,957,781 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,806 duplication rate = 7.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9185 >>>>>>> ACTG content number of A's = 30,061,427 bp (27.34%) number of C's = 19,258,979 bp (17.51%) number of T's = 35,808,564 bp (32.57%) number of G's = 24,802,578 bp (22.56%) number of N's = 26,233 bp (0.02%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,016,317 number of insertions = 7,823 mapped reads with insertion percentage = 0.44% number of deletions = 34,776 mapped reads with deletion percentage = 1.94% homopolymer indels = 49.65% >>>>>>> Coverage mean coverageData = 0.0355X std coverageData = 0.348X There is a 2.59% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 8215639 0.03296135819858198 0.549329319048845 chr2 243199373 11649699 0.047901846358789746 0.39545462646855345 chr3 198022430 7532296 0.03803758998412453 0.25534298548147544 chr4 191154276 7098360 0.03713419416262496 0.2588027109210799 chr5 180915260 6435128 0.03556984634684769 0.24934823246619878 chr6 171115067 6097967 0.03563664560292636 0.29538048665347916 chr7 159138663 6447802 0.040516879295385305 0.5471606633366173 chr8 146364022 6309029 0.04310505350830001 0.5271784236855627 chr9 141213431 4072158 0.028836902914709295 0.2973390155714499 chr10 135534747 5131634 0.03786212844740102 0.3023905879121349 chr11 135006516 4846095 0.035895267455090835 0.30288207806487405 chr12 133851895 5064948 0.037839942422929464 0.2568384191150674 chr13 115169878 2736978 0.0237647034756779 0.2025493746231216 chr14 107349540 3902399 0.03635226569205606 0.25869134042473424 chr15 102531392 2817126 0.027475741283215973 0.22170577733973454 chr16 90354753 3204016 0.03546040350528101 0.25325088099117166 chr17 81195210 2809315 0.034599516400043794 0.25901015783333226 chr18 78077248 2575931 0.03299208240536347 0.4682235293471497 chr19 59128983 1897989 0.03209913148683785 0.380215805236137 chr20 63025520 2294998 0.0364137892079272 0.2529591794829319 chr21 48129895 1779139 0.036965362172512534 0.25794417459447233 chr22 51304566 1018554 0.019853086760348 0.17802521190808127 chrMT 16571 43425 2.6205419105666525 3.4767611827220173 chrX 155270560 5789162 0.03728435061997587 0.2738902412650227 chrY 59373566 248016 0.004177212465224002 0.09173699234343516