BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006047.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 10,165,366 number of mapped reads = 8,761,644 (86.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,470,213 number of mapped paired reads (second in pair) = 4,291,431 number of mapped paired reads (both in pair) = 7,987,536 number of mapped paired reads (singletons) = 774,108 number of mapped bases = 338,492,479 bp number of sequenced bases = 338,456,412 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 592,274 duplication rate = 6.11% >>>>>>> Insert size mean insert size = 58,886.4393 std insert size = 2,396,082.6818 median insert size = 89 >>>>>>> Mapping quality mean mapping quality = 46.742 >>>>>>> ACTG content number of A's = 92,685,272 bp (27.38%) number of C's = 74,110,236 bp (21.9%) number of T's = 95,170,533 bp (28.12%) number of G's = 76,353,286 bp (22.56%) number of N's = 137,085 bp (0.04%) GC percentage = 44.46% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,860,674 number of insertions = 10,619 mapped reads with insertion percentage = 0.12% number of deletions = 28,595 mapped reads with deletion percentage = 0.33% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.1093X std coverageData = 0.6028X There is a 6.1% of reference with a coverageData >= 1X There is a 2.67% of reference with a coverageData >= 2X There is a 1.14% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 28525066 0.11444330965177414 0.6471056541800077 chr2 243199373 29354229 0.12070026595010999 0.6670391683723784 chr3 198022430 23102313 0.1166651323286963 0.5383918991141815 chr4 191154276 21074985 0.1102511826625317 0.5445943675415795 chr5 180915260 20936272 0.11572419043037055 0.5370332963443527 chr6 171115067 20440770 0.11945628376488904 0.6273571583918005 chr7 159138663 18526182 0.11641534276305941 0.7363269108355659 chr8 146364022 17252091 0.11787111862777315 0.6207400834668514 chr9 141213431 14286825 0.10117185666284109 0.5554285813418501 chr10 135534747 16286880 0.12016756116422307 0.5714492494030798 chr11 135006516 15869555 0.11754658567739057 0.9169220209302614 chr12 133851895 15237156 0.113835937847574 0.5374261213804091 chr13 115169878 10861058 0.09430467574169003 0.48747609769787675 chr14 107349540 10463991 0.09747588112627217 0.5080183720092577 chr15 102531392 10444296 0.10186437340087999 0.5092481902821407 chr16 90354753 10425010 0.11537865639453411 0.5882365612301785 chr17 81195210 9997466 0.12312876584714788 0.621706380856124 chr18 78077248 8838299 0.11319941758193117 0.7235160529003706 chr19 59128983 7197149 0.12171947892288287 0.658980478017604 chr20 63025520 7835185 0.12431765735530623 0.5684783398556857 chr21 48129895 4531974 0.09416131076122232 0.5398330227537594 chr22 51304566 4425494 0.08625926199239264 0.5090521838899978 chrMT 16571 32982 1.9903445778770141 3.1422274941193207 chrX 155270560 10379327 0.06684671582301242 0.4368028143908826 chrY 59373566 2167924 0.036513286064037316 0.3346667296131867