BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708597.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 = 4,790,891 number of mapped reads = 4,668,683 (97.45%) number of supplementary alignments = 138 (0%) number of secondary alignments = 0 number of mapped bases = 232,838,321 bp number of sequenced bases = 232,818,439 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,456 duplication rate = 0.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7424 >>>>>>> ACTG content number of A's = 72,024,983 bp (30.94%) number of C's = 44,244,794 bp (19%) number of T's = 71,753,403 bp (30.82%) number of G's = 44,786,999 bp (19.24%) number of N's = 8,260 bp (0%) GC percentage = 38.24% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 334,857 number of insertions = 14,459 mapped reads with insertion percentage = 0.31% number of deletions = 11,671 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.54% >>>>>>> Coverage mean coverageData = 0.0752X std coverageData = 0.3014X There is a 6.99% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 17803191 0.07142686717719351 0.27930856917904023 chr2 243199373 20172042 0.08294446548593692 0.2978798661110296 chr3 198022430 17962526 0.09070955244817469 0.31143803710066653 chr4 191154276 18058068 0.09446855376648755 0.31717362511255043 chr5 180915260 16261594 0.0898851429116593 0.3098212664856677 chr6 171115067 15514859 0.0906691577311541 0.31134885774271226 chr7 159138663 12985174 0.08159660107236165 0.29653028480864096 chr8 146364022 12986510 0.08872747429692797 0.3080660817953151 chr9 141213431 9670824 0.06848374075692559 0.27234656164910376 chr10 135534747 9936507 0.07331335484029051 0.2798346089143839 chr11 135006516 10691429 0.07919194803901168 0.5550461779211343 chr12 133851895 10897000 0.0814108758041864 0.2958423296668532 chr13 115169878 8718417 0.07570049696501371 0.28551552401034985 chr14 107349540 7164777 0.066742503041932 0.26892299939016867 chr15 102531392 6103978 0.05953277216796198 0.253680534968213 chr16 90354753 4164143 0.04608659602002343 0.22225843909547616 chr17 81195210 3807193 0.04688937931190768 0.2248724563497901 chr18 78077248 6633085 0.08495541492446045 0.301016709409615 chr19 59128983 1868883 0.03160688557758553 0.18320452654722605 chr20 63025520 3593621 0.057018506154332405 0.24769142899110194 chr21 48129895 2810775 0.05839977419439623 0.2530458673211046 chr22 51304566 1375725 0.026814864782210613 0.16959267266725805 chrMT 16571 450 0.027155874720897956 0.17156850702408633 chrX 155270560 13347712 0.0859642162686861 0.3034067571935221 chrY 59373566 309838 0.005218450244339375 0.07573828888942034