BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975223.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 4,011,662 number of mapped reads = 3,974,776 (99.08%) number of supplementary alignments = 49,757 (1.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,995,583 number of mapped paired reads (second in pair) = 1,979,193 number of mapped paired reads (both in pair) = 3,955,718 number of mapped paired reads (singletons) = 19,058 number of mapped bases = 565,778,053 bp number of sequenced bases = 565,387,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 537,448 duplication rate = 12.3% >>>>>>> Insert size mean insert size = 92,642.951 std insert size = 2,962,998.6951 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 53.8991 >>>>>>> ACTG content number of A's = 166,557,825 bp (29.46%) number of C's = 115,116,600 bp (20.36%) number of T's = 164,799,625 bp (29.15%) number of G's = 118,860,369 bp (21.02%) number of N's = 52,781 bp (0.01%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 5,092,810 number of insertions = 96,409 mapped reads with insertion percentage = 2.32% number of deletions = 214,734 mapped reads with deletion percentage = 5.21% homopolymer indels = 48.91% >>>>>>> Coverage mean coverageData = 0.1828X std coverageData = 1.9944X There is a 9.7% of reference with a coverageData >= 1X There is a 5.79% of reference with a coverageData >= 2X There is a 1.15% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 56294094 0.22585337510553283 2.1180377427510817 chr2 243199373 48675446 0.20014626435735094 1.769569379765059 chr3 198022430 35621315 0.17988525340285946 0.6504945433277 chr4 191154276 24087865 0.126012692491378 0.9723507450923553 chr5 180915260 33693399 0.18623856826671228 0.6205846430497524 chr6 171115067 42345112 0.24746571264820297 1.0879593617591783 chr7 159138663 37888862 0.2380870951517294 2.2323072695566006 chr8 146364022 40881236 0.27931205662003467 0.9443474745887908 chr9 141213431 23271208 0.16479457963173488 2.1184564564832415 chr10 135534747 25612590 0.18897434471176605 5.846326252810949 chr11 135006516 24025189 0.17795577363095572 1.9730006940481923 chr12 133851895 27026994 0.20191715627186302 0.6487415044610206 chr13 115169878 11395018 0.0989409574611167 0.43670056279864006 chr14 107349540 16155594 0.150495232676358 0.5612760995734178 chr15 102531392 10890017 0.10621153958389641 0.4576691485007206 chr16 90354753 19787896 0.21900226986398824 4.508908181462879 chr17 81195210 13229707 0.1629370377883129 2.404757835910222 chr18 78077248 20332006 0.26040884535274605 2.0780467412718764 chr19 59128983 12725764 0.21522041060641953 1.4663357989158137 chr20 63025520 12004452 0.19046970179698636 0.7036546013289172 chr21 48129895 6884499 0.14303997546639152 0.776234834407236 chr22 51304566 3710697 0.07232683734231374 0.388121561158982 chrMT 16571 34427 2.077545108925231 2.255036550257386 chrX 155270560 15740992 0.10137782719402828 0.6997828640515547 chrY 59373566 3463674 0.058336971035224665 1.4477213524052306