BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708621.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,315,477 number of mapped reads = 3,164,630 (73.33%) number of supplementary alignments = 957 (0.02%) number of secondary alignments = 0 number of mapped bases = 154,161,422 bp number of sequenced bases = 154,131,932 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,976 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1757 >>>>>>> ACTG content number of A's = 45,401,812 bp (29.46%) number of C's = 29,027,912 bp (18.83%) number of T's = 48,707,333 bp (31.6%) number of G's = 30,981,629 bp (20.1%) number of N's = 13,246 bp (0.01%) GC percentage = 38.93% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 997,934 number of insertions = 7,404 mapped reads with insertion percentage = 0.23% number of deletions = 19,372 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.11% >>>>>>> Coverage mean coverageData = 0.0498X std coverageData = 0.5079X There is a 4.1% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 11913333 0.0477966030824854 0.9195265038421875 chr2 243199373 13089789 0.05382328432236542 0.5477942855907645 chr3 198022430 10810542 0.054592512575469355 0.27881136222813446 chr4 191154276 10586911 0.05538411811410381 0.28384137351001804 chr5 180915260 10183672 0.056289734763115065 0.2884178195742561 chr6 171115067 9085205 0.05309412642195909 0.37733401276408274 chr7 159138663 8883228 0.055820677593602756 0.7932044873620518 chr8 146364022 8013853 0.05475288865729585 0.8984446061926679 chr9 141213431 6530142 0.046243065930463796 0.4013753114116341 chr10 135534747 6686787 0.049336329967104305 0.4007907967247081 chr11 135006516 7197142 0.05330958988675776 0.4182452259700294 chr12 133851895 7159289 0.05348664656559401 0.2841329227784083 chr13 115169878 5471865 0.04751125116239161 0.2619314973116193 chr14 107349540 4723648 0.04400249875313858 0.27778561437848887 chr15 102531392 4288330 0.0418245565221625 0.2406513772674522 chr16 90354753 3850786 0.042618521684188546 0.26449104796033013 chr17 81195210 3301915 0.04066637674808649 0.2877657279255664 chr18 78077248 4337941 0.055559604252444966 0.8412280683147035 chr19 59128983 2532554 0.04283100894869103 0.7093739150617696 chr20 63025520 2841024 0.04507735913959932 0.26346156784868696 chr21 48129895 2093727 0.04350159085117472 0.2706594468245735 chr22 51304566 1552179 0.03025420778337741 0.20181134066768178 chrMT 16571 8516 0.5139098424959266 0.8894456807763124 chrX 155270560 8664804 0.055804551745031385 0.3235024353171299 chrY 59373566 354240 0.005966291463780363 0.10592136658999425