BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818821.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,872,733 number of mapped reads = 1,824,540 (97.43%) number of supplementary alignments = 12,084 (0.65%) number of secondary alignments = 0 number of mapped bases = 123,877,866 bp number of sequenced bases = 123,828,770 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 794,289 duplication rate = 36.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7523 >>>>>>> ACTG content number of A's = 34,938,205 bp (28.21%) number of C's = 28,002,642 bp (22.61%) number of T's = 35,490,205 bp (28.66%) number of G's = 25,389,370 bp (20.5%) number of N's = 8,348 bp (0.01%) GC percentage = 43.12% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 629,348 number of insertions = 13,567 mapped reads with insertion percentage = 0.73% number of deletions = 30,725 mapped reads with deletion percentage = 1.67% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.4784X There is a 1.9% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% 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 0.01% 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 10313269 0.041377104532870954 0.7054235084964867 chr2 243199373 11016126 0.045296687504206685 0.6966346334905116 chr3 198022430 8536927 0.043110909203568505 0.3804522957905677 chr4 191154276 8177115 0.04277756779032241 0.41962927421214635 chr5 180915260 7637472 0.04221574233152029 0.387845752314107 chr6 171115067 7299230 0.042656851485789966 0.4143023670387919 chr7 159138663 6900537 0.043361788203536686 0.46645939873719217 chr8 146364022 5936140 0.040557371401012746 0.42357676189879456 chr9 141213431 5280201 0.03739163451102608 0.4091858419833255 chr10 135534747 5818597 0.04293066633311383 0.4731746573283649 chr11 135006516 5707112 0.04227286333350014 0.41063339327430304 chr12 133851895 5645109 0.04217429271359961 0.3986919618475658 chr13 115169878 3910783 0.03395664793532212 0.3355959847080787 chr14 107349540 3770726 0.03512568381755525 0.3673837949010423 chr15 102531392 3669268 0.035786776405025304 0.3517608470582405 chr16 90354753 3725160 0.04122815763770612 0.5150529570138528 chr17 81195210 3480534 0.04286624789812108 0.40718839234662607 chr18 78077248 3368133 0.04313846973704811 0.5021867977108989 chr19 59128983 2625188 0.04439765182499418 0.6090236968594857 chr20 63025520 2793018 0.044315667685090106 0.4086458040436977 chr21 48129895 1664319 0.03457973469503725 0.3602212325409669 chr22 51304566 1563827 0.03048124410603142 0.349905581340097 chrMT 16571 124870 7.535453503107839 6.782740736383553 chrX 155270560 3828971 0.024659993497801513 0.3162646346092802 chrY 59373566 1085234 0.018278066707328983 0.6982980647872257