BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004163.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 = 2,094,207 number of mapped reads = 1,757,579 (83.93%) number of supplementary alignments = 23,943 (1.14%) number of secondary alignments = 0 number of mapped bases = 113,602,716 bp number of sequenced bases = 113,530,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,763 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5479 >>>>>>> ACTG content number of A's = 31,992,537 bp (28.18%) number of C's = 20,849,281 bp (18.36%) number of T's = 36,014,298 bp (31.72%) number of G's = 24,657,403 bp (21.72%) number of N's = 17,052 bp (0.02%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,127,952 number of insertions = 8,462 mapped reads with insertion percentage = 0.48% number of deletions = 42,689 mapped reads with deletion percentage = 2.39% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.0367X std coverageData = 0.3476X There is a 3.05% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 9142709 0.03668078724666447 0.6358016036249321 chr2 243199373 7932711 0.032618139192324314 0.34090029852887505 chr3 198022430 8618844 0.043524584563475965 0.24101406713154433 chr4 191154276 8023757 0.04197529434287936 0.2586214699040624 chr5 180915260 5839333 0.03227661945155981 0.21087790079820498 chr6 171115067 7205440 0.04210874078084544 0.2603821364263479 chr7 159138663 7788355 0.048940683886479555 0.4771160805707834 chr8 146364022 7593450 0.05188057759167072 0.5541643658312821 chr9 141213431 4511521 0.031948242940149224 0.30090951105377994 chr10 135534747 5414184 0.03994683370752151 0.34867795686380165 chr11 135006516 4755644 0.0352252923851468 0.2659668112795222 chr12 133851895 4471841 0.033408873292380355 0.21878780948318705 chr13 115169878 4080665 0.03543170376545853 0.21992106005551548 chr14 107349540 2844515 0.026497691559740265 0.2121231293619794 chr15 102531392 3734649 0.03642444452524355 0.22121441888220306 chr16 90354753 3002272 0.0332276045290058 0.23977640146536514 chr17 81195210 2608269 0.03212343437500808 0.23144883357353063 chr18 78077248 2612111 0.03345546963950369 0.48791943136881116 chr19 59128983 1658261 0.02804480841485131 0.44007300524296367 chr20 63025520 2277199 0.036131379796628414 0.23182790799460626 chr21 48129895 1506487 0.031300442271897745 0.23061696772810283 chr22 51304566 748584 0.014590982019027312 0.13724293199362514 chrMT 16571 14737 0.8893247239152736 1.1497519217837824 chrX 155270560 6880226 0.044311207481959235 0.27071449227113287 chrY 59373566 336952 0.005675118115694786 0.14445633011016243