BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240020.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 = 2,674,260 number of mapped reads = 2,088,737 (78.11%) number of supplementary alignments = 18,142 (0.68%) number of secondary alignments = 0 number of mapped bases = 138,150,092 bp number of sequenced bases = 138,082,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,282 duplication rate = 11.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.825 >>>>>>> ACTG content number of A's = 38,999,277 bp (28.24%) number of C's = 25,485,517 bp (18.46%) number of T's = 44,137,684 bp (31.96%) number of G's = 29,447,312 bp (21.33%) number of N's = 12,934 bp (0.01%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,177,436 number of insertions = 9,978 mapped reads with insertion percentage = 0.47% number of deletions = 38,201 mapped reads with deletion percentage = 1.81% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.5073X There is a 1.89% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% 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 11112261 0.04458268130052121 0.6676963985253159 chr2 243199373 14896743 0.06125321301712402 0.5853016939395892 chr3 198022430 8880933 0.04484811644822256 0.4194086483905883 chr4 191154276 9078088 0.047490896829323344 0.43929619952776927 chr5 180915260 7403198 0.0409208045800006 0.40109883917577643 chr6 171115067 7293124 0.04262116789516846 0.4480303769558236 chr7 159138663 8316636 0.05226031087115517 0.8052281914367152 chr8 146364022 7860508 0.05370519265998307 0.679612993631384 chr9 141213431 5127284 0.036308755928464054 0.4291518597130776 chr10 135534747 6265983 0.0462315615640615 0.48941618279346005 chr11 135006516 6017841 0.04457444853995047 0.4808377660537683 chr12 133851895 6843639 0.0511284431199125 0.44941095491748695 chr13 115169878 3562124 0.03092930253863775 0.3479781143242759 chr14 107349540 4368587 0.04069497642933542 0.3993789284083283 chr15 102531392 3935530 0.03838365912363698 0.3894995521071465 chr16 90354753 4021066 0.044503093268375156 0.4097894572317086 chr17 81195210 3196729 0.03937090623941979 0.40471293345871245 chr18 78077248 3533353 0.045254579157298164 0.6507138273972942 chr19 59128983 2313420 0.039124975310331316 0.5043503694131343 chr20 63025520 2800575 0.0444355714954831 0.4169387681448481 chr21 48129895 2196083 0.04562825246138601 0.41632939310812533 chr22 51304566 1301371 0.02536559806392281 0.3020356864114959 chrMT 16571 25696 1.550660792951542 2.8860703772606886 chrX 155270560 7439075 0.04791040233254778 0.4440719760052054 chrY 59373566 360245 0.006067430748559048 0.14308952865942548