BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081108.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,265,123 number of mapped reads = 2,067,268 (91.27%) number of supplementary alignments = 20,635 (0.91%) number of secondary alignments = 0 number of mapped bases = 139,359,500 bp number of sequenced bases = 139,308,775 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,905 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3467 >>>>>>> ACTG content number of A's = 38,628,788 bp (27.73%) number of C's = 26,502,628 bp (19.02%) number of T's = 43,218,616 bp (31.02%) number of G's = 30,957,160 bp (22.22%) number of N's = 1,583 bp (0%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,247,574 number of insertions = 11,232 mapped reads with insertion percentage = 0.54% number of deletions = 31,070 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.3843X There is a 3.82% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 11761704 0.047188263575078514 0.6622987829210669 chr2 243199373 10054598 0.04134302599538363 0.39788937570237204 chr3 198022430 12105509 0.061132009136540745 0.28109358201821705 chr4 191154276 8155593 0.042664978103864125 0.25308955119818843 chr5 180915260 7105569 0.039275675252601686 0.22784128591826705 chr6 171115067 11609070 0.0678436458199207 0.44913133414122536 chr7 159138663 6798351 0.04271966894682281 0.45635409208577843 chr8 146364022 9522566 0.06506083851672237 0.4134759143478475 chr9 141213431 6956364 0.04926134823535305 0.4115607205964775 chr10 135534747 6354692 0.04688607269101259 0.3816202488724309 chr11 135006516 6048418 0.04480093390455317 0.30145287979568786 chr12 133851895 7129448 0.053263706128329376 0.27472468804414757 chr13 115169878 3835619 0.033304012009112316 0.20785204334163404 chr14 107349540 3735580 0.03479828604761604 0.27809093681465524 chr15 102531392 3764598 0.03671654043280716 0.21711562085023417 chr16 90354753 3840981 0.042510004980036854 0.28587423812029844 chr17 81195210 2940229 0.03621185289132204 0.22335380638349756 chr18 78077248 3427523 0.04389912667003837 0.6825901275161189 chr19 59128983 2949178 0.049877029002849585 0.5163340302060685 chr20 63025520 2365227 0.03752808386190229 0.23671816543067514 chr21 48129895 3269870 0.06793844033941898 0.3371755875767278 chr22 51304566 1265688 0.02467008491992701 0.17603605809349582 chrMT 16571 416113 25.110916661637802 12.910333739591032 chrX 155270560 3611565 0.023259818216666443 0.1967319848255845 chrY 59373566 335447 0.005649770135079979 0.15244060251579242