BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926973.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 20,356,400 number of mapped reads = 19,934,921 (97.93%) number of supplementary alignments = 692,186 (3.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,006,169 number of mapped paired reads (second in pair) = 9,928,752 number of mapped paired reads (both in pair) = 19,665,408 number of mapped paired reads (singletons) = 269,513 number of mapped bases = 1,784,773,717 bp number of sequenced bases = 1,783,363,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,926,365 duplication rate = 7.77% >>>>>>> Insert size mean insert size = 373,177.8558 std insert size = 5,986,098.1423 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 52.5145 >>>>>>> ACTG content number of A's = 511,018,712 bp (28.65%) number of C's = 339,547,513 bp (19.04%) number of T's = 525,502,404 bp (29.47%) number of G's = 407,160,865 bp (22.83%) number of N's = 134,226 bp (0.01%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 17,024,375 number of insertions = 318,617 mapped reads with insertion percentage = 1.57% number of deletions = 954,458 mapped reads with deletion percentage = 4.67% homopolymer indels = 51.67% >>>>>>> Coverage mean coverageData = 0.5765X std coverageData = 2.1627X There is a 27.02% of reference with a coverageData >= 1X There is a 13.29% of reference with a coverageData >= 2X There is a 6.67% of reference with a coverageData >= 3X There is a 3.73% of reference with a coverageData >= 4X There is a 2.16% of reference with a coverageData >= 5X There is a 1.32% of reference with a coverageData >= 6X There is a 0.83% of reference with a coverageData >= 7X There is a 0.55% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 141725335 0.5686057448177833 2.3510019352446485 chr2 243199373 162844334 0.6695919154363938 3.756596786262904 chr3 198022430 130052909 0.6567584742799086 1.4288986834013386 chr4 191154276 112279561 0.5873766642813683 2.0251607997508514 chr5 180915260 109420457 0.6048160724529263 1.3520113923138846 chr6 171115067 106360260 0.6215715650568632 1.6612945960209766 chr7 159138663 90961044 0.5715835629459826 2.0270227757610044 chr8 146364022 90219121 0.616402308212055 1.6540007151642548 chr9 141213431 73815225 0.5227209938692021 2.4370119619626522 chr10 135534747 87096492 0.6426137498157576 2.857013469629723 chr11 135006516 84731923 0.627613581258552 2.855552506738275 chr12 133851895 83093738 0.6207886559992296 1.668616046622022 chr13 115169878 41511622 0.36043818679741935 1.091132727472026 chr14 107349540 55488841 0.516898731005275 1.3234561435732524 chr15 102531392 52722415 0.514207541432774 1.361449386197232 chr16 90354753 54411050 0.6021935558829982 2.8286164390726927 chr17 81195210 44038304 0.5423756401393629 1.6012752432783695 chr18 78077248 46248779 0.5923464285011685 2.5844756115594354 chr19 59128983 26392764 0.44635917380821516 1.6606293129996965 chr20 63025520 39965129 0.634110262001805 1.5148671997044443 chr21 48129895 21772862 0.45237709328058995 1.7119764140780316 chr22 51304566 20478765 0.3991606711963999 1.1970758095435028 chrMT 16571 371960 22.446442580411563 20.991013713099047 chrX 155270560 105540859 0.6797222796130831 1.7107888403911657 chrY 59373566 3229968 0.05440077491724179 1.8897184002831116