BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084801.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 = 1,587,073 number of mapped reads = 1,465,223 (92.32%) number of supplementary alignments = 14,152 (0.89%) number of secondary alignments = 0 number of mapped bases = 99,489,313 bp number of sequenced bases = 99,449,837 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,775 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4545 >>>>>>> ACTG content number of A's = 27,985,989 bp (28.14%) number of C's = 18,175,441 bp (18.28%) number of T's = 31,878,585 bp (32.05%) number of G's = 21,395,901 bp (21.51%) number of N's = 13,921 bp (0.01%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 759,344 number of insertions = 8,532 mapped reads with insertion percentage = 0.58% number of deletions = 23,812 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.83% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.2613X There is a 2.73% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 8224577 0.032997217687975186 0.3440278648315587 chr2 243199373 7661861 0.03150444388686808 0.3271553248528329 chr3 198022430 8314517 0.04198775360952797 0.23513628164318126 chr4 191154276 6763379 0.03538178240909453 0.21763551142499502 chr5 180915260 4882035 0.026985202906598373 0.18932171043747867 chr6 171115067 5863087 0.03426400201216647 0.2243076075969942 chr7 159138663 6233992 0.03917333401248947 0.30478478573897205 chr8 146364022 5363642 0.03664590468824367 0.30454037881948776 chr9 141213431 7264674 0.05144463914342539 0.33867368800819725 chr10 135534747 3143802 0.023195542616093863 0.1913016050419351 chr11 135006516 2815849 0.020857134036404584 0.19601668453662235 chr12 133851895 3948764 0.029500994363957266 0.20008542549657896 chr13 115169878 2819618 0.024482252208342183 0.17888880236485816 chr14 107349540 2474926 0.023054835633203458 0.18188341937812796 chr15 102531392 2188857 0.021348164277336643 0.17220240473855383 chr16 90354753 1657732 0.01834692636479234 0.16686664761511455 chr17 81195210 2480150 0.030545521096626265 0.20119489063573015 chr18 78077248 4061569 0.0520198790818037 0.5529137163973609 chr19 59128983 2130046 0.036023721226526084 0.2768972433288356 chr20 63025520 1857126 0.029466254304605498 0.2003855939378613 chr21 48129895 1011528 0.02101662594526749 0.17164780631438845 chr22 51304566 1109978 0.021635072402717528 0.16514346077240863 chrMT 16571 12838 0.7747269325930843 1.0412326104968683 chrX 155270560 6987390 0.045001383391674504 0.2560435965959982 chrY 59373566 217376 0.003661157896428185 0.07759968984249901