BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008742.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 = 1,369,866 number of mapped reads = 1,118,515 (81.65%) number of supplementary alignments = 6,326 (0.46%) number of secondary alignments = 0 number of mapped bases = 75,757,164 bp number of sequenced bases = 75,716,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,968 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6126 >>>>>>> ACTG content number of A's = 23,039,579 bp (30.43%) number of C's = 13,585,711 bp (17.94%) number of T's = 22,560,728 bp (29.8%) number of G's = 16,523,697 bp (21.82%) number of N's = 7,248 bp (0.01%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 646,196 number of insertions = 6,321 mapped reads with insertion percentage = 0.56% number of deletions = 24,386 mapped reads with deletion percentage = 2.15% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.1962X There is a 2.3% of reference with a coverageData >= 1X There is a 0.11% 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 5855109 0.023490850199326084 0.26229750730234225 chr2 243199373 7318586 0.030092947649170133 0.22799935267457594 chr3 198022430 6024331 0.030422467798218614 0.18209100867726952 chr4 191154276 4221142 0.02208238334150579 0.15698922077167313 chr5 180915260 3322637 0.018365708895977044 0.1406630149830676 chr6 171115067 3928656 0.022959147133431564 0.16768533082928344 chr7 159138663 3755454 0.02359862731786304 0.21055043575609247 chr8 146364022 6160779 0.042092167978275426 0.2587431687551278 chr9 141213431 2650123 0.01876679138261289 0.17736549830458448 chr10 135534747 4534495 0.033456328361316824 0.23389518735622308 chr11 135006516 3181953 0.023568884630724048 0.2073614586369315 chr12 133851895 3533489 0.02639849813108735 0.1688597905526974 chr13 115169878 1747678 0.015174783809356818 0.1274414774819647 chr14 107349540 3363280 0.03133017617029379 0.18591344799144943 chr15 102531392 2136361 0.02083616498642679 0.15000381420485054 chr16 90354753 1904983 0.021083373444670917 0.16308725042608502 chr17 81195210 2003015 0.024669127649278817 0.18276783763608712 chr18 78077248 1233585 0.015799545086425178 0.29390545466460255 chr19 59128983 1378017 0.023305271460528926 0.2044009129478888 chr20 63025520 1281936 0.020339951181680055 0.15060432075581598 chr21 48129895 799237 0.016605833027476997 0.13826357221806324 chr22 51304566 873938 0.017034312306627834 0.13535502893327386 chrMT 16571 20229 1.2207470882867661 1.3703190435040533 chrX 155270560 4368165 0.028132602857875954 0.18443403321211482 chrY 59373566 159986 0.0026945661306582123 0.0755165591542917