BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238276.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 = 3,155,276 number of mapped reads = 2,837,094 (89.92%) number of supplementary alignments = 25,328 (0.8%) number of secondary alignments = 0 number of mapped bases = 185,232,696 bp number of sequenced bases = 185,136,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,672 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1429 >>>>>>> ACTG content number of A's = 51,122,510 bp (27.61%) number of C's = 35,205,432 bp (19.02%) number of T's = 56,677,332 bp (30.61%) number of G's = 42,086,225 bp (22.73%) number of N's = 45,342 bp (0.02%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,633,660 number of insertions = 15,228 mapped reads with insertion percentage = 0.53% number of deletions = 57,808 mapped reads with deletion percentage = 2.01% homopolymer indels = 45.24% >>>>>>> Coverage mean coverageData = 0.0598X std coverageData = 0.5121X There is a 4.86% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 14029965 0.056288585936963426 0.8497581711129907 chr2 243199373 13076613 0.053769106551109405 0.6782476780818731 chr3 198022430 12267363 0.06194936098905563 0.29638602549501886 chr4 191154276 10404992 0.05443243132055283 0.31408027970129265 chr5 180915260 11977014 0.06620234246685437 0.30552838157831314 chr6 171115067 9792186 0.05722573804678462 0.3717336746837296 chr7 159138663 12338469 0.07753281803052474 0.7829455005790904 chr8 146364022 13079165 0.08936051921284317 0.6855016940372002 chr9 141213431 9417540 0.0666901153332929 0.5006623083417313 chr10 135534747 6423828 0.047396170666109703 0.4852953483217598 chr11 135006516 6057135 0.04486550115847742 0.387523317676466 chr12 133851895 7453667 0.05568592809238898 0.28628513246867293 chr13 115169878 6445848 0.055968175984348965 0.27844999453953495 chr14 107349540 5885937 0.05482964342464812 0.3153482865303831 chr15 102531392 5549425 0.054124155458652116 0.282088914466929 chr16 90354753 5891042 0.06519902721664238 0.3509490294551221 chr17 81195210 5214033 0.0642160171763827 0.3780543198848765 chr18 78077248 5132081 0.06573081315570958 0.8886948456612225 chr19 59128983 2896522 0.04898650125607606 0.6512242156045902 chr20 63025520 4363595 0.06923536687995593 0.3211910529617272 chr21 48129895 2148378 0.04463708055045622 0.29150600553036293 chr22 51304566 2244815 0.04375468257542613 0.246782633035553 chrMT 16571 7119 0.4296059380846056 0.812517905686715 chrX 155270560 12604784 0.08117948437875151 0.3926648250414345 chrY 59373566 531180 0.00894640554350399 0.21951685714557684