BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240036.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 = 1,699,314 number of mapped reads = 1,287,538 (75.77%) number of supplementary alignments = 10,623 (0.63%) number of secondary alignments = 0 number of mapped bases = 80,268,040 bp number of sequenced bases = 80,234,179 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,427 duplication rate = 9.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4579 >>>>>>> ACTG content number of A's = 21,735,400 bp (27.09%) number of C's = 14,373,694 bp (17.91%) number of T's = 25,693,270 bp (32.02%) number of G's = 18,380,323 bp (22.91%) number of N's = 51,492 bp (0.06%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 738,248 number of insertions = 6,496 mapped reads with insertion percentage = 0.5% number of deletions = 19,930 mapped reads with deletion percentage = 1.53% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 0.0259X std coverageData = 0.368X There is a 1.69% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 10094539 0.04049955406129159 0.7818382538927303 chr2 243199373 5469024 0.022487821134308597 0.45030698603589087 chr3 198022430 5195549 0.02623717424334203 0.2325943052671741 chr4 191154276 3557882 0.018612620520191765 0.23335996850083288 chr5 180915260 6249423 0.03454337129991135 0.268853172140201 chr6 171115067 4263049 0.024913346759815137 0.2482766726364389 chr7 159138663 3928503 0.024686037484178185 0.2686839439334577 chr8 146364022 4692670 0.03206163602145341 0.39815348617860447 chr9 141213431 7206453 0.05103234833236224 0.44325512133275435 chr10 135534747 2466598 0.01819900840630927 0.29726179136563197 chr11 135006516 3192772 0.02364902150352506 0.2554791104554307 chr12 133851895 3071244 0.022945091662691812 0.23390995374949955 chr13 115169878 2306328 0.02002544450034062 0.2043916254382864 chr14 107349540 1665853 0.015518026439610267 0.22032695066980199 chr15 102531392 1559785 0.015212755523693661 0.18524788513102725 chr16 90354753 1960893 0.02170215660929315 0.23706493383876076 chr17 81195210 1670525 0.020574181654311872 0.22852501405713083 chr18 78077248 2345981 0.030046922248079234 0.5236769807073149 chr19 59128983 3093691 0.05232105886211505 0.596606305615821 chr20 63025520 1547750 0.02455751257585816 0.23226025255703245 chr21 48129895 863086 0.017932430561088904 0.22633275984038825 chr22 51304566 503751 0.009818833668722585 0.13499897970688815 chrMT 16571 26506 1.599541367449158 2.1011871319073303 chrX 155270560 3110304 0.020031511446857667 0.2325472346132443 chrY 59373566 225881 0.003804403461297912 0.1428319211626232