BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524971.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 = 743,013 number of mapped reads = 690,971 (93%) number of supplementary alignments = 1,757 (0.24%) number of secondary alignments = 0 number of mapped bases = 40,718,654 bp number of sequenced bases = 40,704,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,170 duplication rate = 1.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.735 >>>>>>> ACTG content number of A's = 10,616,022 bp (26.08%) number of C's = 7,613,712 bp (18.7%) number of T's = 12,191,016 bp (29.95%) number of G's = 10,283,752 bp (25.26%) number of N's = 447 bp (0%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 196,925 number of insertions = 2,420 mapped reads with insertion percentage = 0.35% number of deletions = 7,936 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.0132X std coverageData = 0.1472X There is a 1.24% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4022681 0.01613910121411493 0.23603652040261194 chr2 243199373 3932660 0.01617051866330264 0.16760063431827688 chr3 198022430 2264158 0.011433846155710744 0.11130742043914274 chr4 191154276 2650210 0.013864246489573689 0.12574136395436855 chr5 180915260 1781278 0.009845924550532664 0.1034140882857539 chr6 171115067 2776916 0.016228354689537657 0.1667355375791567 chr7 159138663 2602774 0.01635538436061889 0.18774218035984327 chr8 146364022 2465316 0.016843729533477837 0.15162322604172282 chr9 141213431 1151208 0.008152255715676224 0.11751646316225306 chr10 135534747 2067316 0.015253033231397112 0.15121327293326797 chr11 135006516 1720373 0.01274288864694501 0.1373228502410441 chr12 133851895 2247927 0.01679413653426423 0.13503536716129483 chr13 115169878 802232 0.006965640790207314 0.0878241066091244 chr14 107349540 939428 0.008751113418837194 0.0983098819511706 chr15 102531392 1147013 0.011186944579860966 0.11114992417804996 chr16 90354753 1309064 0.014488048016688175 0.129028777126826 chr17 81195210 1055233 0.01299624694609448 0.13693473807037312 chr18 78077248 809258 0.010364837654114039 0.16658388245088884 chr19 59128983 994745 0.016823306431636074 0.18308278066536635 chr20 63025520 996093 0.015804597883524008 0.13120146058790613 chr21 48129895 598608 0.012437342736775138 0.11706419538470221 chr22 51304566 552751 0.010773914352964218 0.107288351472611 chrMT 16571 7388 0.44583911652887576 0.718124342968603 chrX 155270560 1718562 0.011068176736143671 0.11939206247337442 chrY 59373566 105462 0.0017762450043846112 0.056015560679731465