BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124935.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,840,704 number of mapped reads = 6,543,398 (95.65%) number of supplementary alignments = 7,478 (0.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,310,289 number of mapped paired reads (second in pair) = 3,233,109 number of mapped paired reads (both in pair) = 6,446,636 number of mapped paired reads (singletons) = 96,762 number of mapped bases = 406,576,105 bp number of sequenced bases = 406,392,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 549,222 duplication rate = 6.44% >>>>>>> Insert size mean insert size = 27,095.7625 std insert size = 1,557,799.5043 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.1964 >>>>>>> ACTG content number of A's = 109,424,446 bp (26.93%) number of C's = 74,621,793 bp (18.36%) number of T's = 118,335,965 bp (29.12%) number of G's = 104,007,199 bp (25.59%) number of N's = 3,274 bp (0%) GC percentage = 43.95% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,707,980 number of insertions = 43,795 mapped reads with insertion percentage = 0.66% number of deletions = 122,439 mapped reads with deletion percentage = 1.85% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.1313X std coverageData = 0.7958X There is a 9.28% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 29069189 0.11662634533616668 0.7604467409101419 chr2 243199373 38426858 0.1580055800555045 1.227182149599928 chr3 198022430 24694429 0.12470521142478658 0.46313638599319423 chr4 191154276 22811110 0.11933350630356812 0.5719936346391573 chr5 180915260 27701839 0.15312052172934446 0.5342677966116319 chr6 171115067 20569907 0.12021096307083233 0.6096729091501462 chr7 159138663 25290378 0.15892038756163235 1.0535324537125934 chr8 146364022 25823590 0.17643400097327197 0.6149111452244594 chr9 141213431 12822032 0.09079895523535576 0.6630555383061786 chr10 135534747 25476742 0.18797203347419095 1.5427229921262577 chr11 135006516 21250721 0.15740515072620642 0.6374610376010855 chr12 133851895 15177586 0.11339089371876282 0.4486691558371634 chr13 115169878 13673555 0.11872509754677348 0.4545888118311833 chr14 107349540 9262156 0.08628035108487657 0.43193065511708695 chr15 102531392 14384908 0.14029759783228146 0.5046982522325484 chr16 90354753 14652329 0.16216445193536194 1.307722479435635 chr17 81195210 15679990 0.193114716988847 0.9485687052016032 chr18 78077248 7058177 0.09039992034555316 0.9548704252382396 chr19 59128983 6801018 0.1150200401721775 0.6714971899498087 chr20 63025520 8657615 0.13736681585491084 0.5601882192227373 chr21 48129895 3354054 0.06968754035303838 0.42837992868844027 chr22 51304566 5488625 0.10698121878664757 0.4571010730193236 chrMT 16571 351420 21.20692776537324 14.625865506517856 chrX 155270560 17185715 0.11068237919667451 0.5049270747949954 chrY 59373566 912162 0.015363099464162217 0.8499895209570827