BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505918.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,714,736 number of mapped reads = 4,603,718 (68.56%) number of supplementary alignments = 219 (0%) number of secondary alignments = 0 number of mapped bases = 212,049,304 bp number of sequenced bases = 212,004,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 212,824 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4507 >>>>>>> ACTG content number of A's = 62,913,077 bp (29.68%) number of C's = 42,985,632 bp (20.28%) number of T's = 62,462,041 bp (29.46%) number of G's = 43,642,850 bp (20.59%) number of N's = 722 bp (0%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,075,526 number of insertions = 9,755 mapped reads with insertion percentage = 0.21% number of deletions = 32,168 mapped reads with deletion percentage = 0.7% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0685X std coverageData = 0.5821X There is a 5.57% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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% 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 22660718 0.090915392343195 1.1526364538359697 chr2 243199373 14100311 0.05797840194267277 0.3980383054062416 chr3 198022430 14490214 0.07317460956316918 0.32226495952916057 chr4 191154276 9610302 0.050275108677139926 0.26910040013434877 chr5 180915260 12490477 0.06904048337326547 0.3130666259804332 chr6 171115067 15462675 0.09036419335300264 0.44761706822029795 chr7 159138663 14646708 0.09203739508607031 1.1360517758423616 chr8 146364022 13495028 0.09220181172665506 0.7764382574431652 chr9 141213431 6062636 0.042932431830793774 0.34136916494244174 chr10 135534747 7179144 0.05296902941059092 0.6244855441275404 chr11 135006516 9122401 0.06757007935824372 0.44624183821078195 chr12 133851895 6518423 0.048698772624773075 0.28014299729756775 chr13 115169878 6335640 0.055011259107177315 0.2743072396350294 chr14 107349540 8394650 0.07819921724862537 0.5597534162482211 chr15 102531392 3956744 0.03859056161063336 0.22741166483760963 chr16 90354753 7335463 0.08118513698997108 0.39596248762346636 chr17 81195210 3709059 0.045680761217318115 0.2887461642527404 chr18 78077248 5172369 0.06624681494921543 0.6400119377825769 chr19 59128983 5225464 0.08837398742339268 0.8749165310582854 chr20 63025520 5347694 0.08484966089926747 0.3522826819085732 chr21 48129895 3306882 0.06870744264037974 0.3256201382943058 chr22 51304566 1655171 0.03226167043299811 0.21006787508574085 chrMT 16571 168142 10.146762416269386 7.035105342905209 chrX 155270560 14955213 0.09631711896962308 0.4120227524217444 chrY 59373566 647776 0.010910175076902067 0.14536363543630842