BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818778.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 = 2,378,435 number of mapped reads = 2,311,997 (97.21%) number of supplementary alignments = 19,093 (0.8%) number of secondary alignments = 0 number of mapped bases = 157,020,343 bp number of sequenced bases = 156,955,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,249,507 duplication rate = 45.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5838 >>>>>>> ACTG content number of A's = 44,265,738 bp (28.2%) number of C's = 33,370,417 bp (21.26%) number of T's = 45,690,979 bp (29.11%) number of G's = 33,618,523 bp (21.42%) number of N's = 9,558 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 793,894 number of insertions = 16,065 mapped reads with insertion percentage = 0.69% number of deletions = 40,489 mapped reads with deletion percentage = 1.73% homopolymer indels = 41.47% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.643X There is a 1.93% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 12849229 0.051551442273036506 0.8643473270391617 chr2 243199373 13768853 0.0566154954684032 1.0466050403661198 chr3 198022430 10520514 0.053127890613199724 0.48257065514641617 chr4 191154276 10556404 0.05522452450919801 0.56347467705472 chr5 180915260 9826956 0.05431800501516566 0.5067187585505037 chr6 171115067 9317015 0.0544488288690557 0.5405002505351812 chr7 159138663 8697817 0.05465558674449841 0.5583661036655644 chr8 146364022 8114010 0.055437189338784366 0.5640612040230183 chr9 141213431 6808417 0.048213664605316474 0.5207780867065098 chr10 135534747 7447342 0.05494784300589722 0.677947673866368 chr11 135006516 7432729 0.05505459455008824 0.5417385513582698 chr12 133851895 7102445 0.05306196822988572 0.515315260952394 chr13 115169878 5125287 0.0445019747264124 0.44447134183075754 chr14 107349540 4871539 0.04538015719489809 0.4876479815175915 chr15 102531392 4450149 0.04340279511664096 0.4364294755336766 chr16 90354753 4681979 0.05181773890743744 0.7244947542442858 chr17 81195210 4226561 0.05205431453407165 0.5097629843989202 chr18 78077248 4333401 0.05550145671117916 0.677832408877389 chr19 59128983 3100097 0.05242939828679279 0.7780380640164629 chr20 63025520 3353980 0.053216220984769344 0.5167312109747331 chr21 48129895 2132078 0.04429841369901181 0.4618363305621763 chr22 51304566 1852520 0.036108287125945084 0.4449912572386658 chrMT 16571 159888 9.648663327499849 9.507478415444956 chrX 155270560 4774165 0.03074739345307958 0.39691068131481866 chrY 59373566 1516968 0.025549551798859444 1.1539787600620506