BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080681.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 = 1,324,307 number of mapped reads = 1,201,981 (90.76%) number of supplementary alignments = 11,065 (0.84%) number of secondary alignments = 0 number of mapped bases = 79,665,734 bp number of sequenced bases = 79,635,798 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,790 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9265 >>>>>>> ACTG content number of A's = 21,699,790 bp (27.25%) number of C's = 14,463,447 bp (18.16%) number of T's = 25,477,775 bp (31.99%) number of G's = 17,991,416 bp (22.59%) number of N's = 3,370 bp (0%) GC percentage = 40.75% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 546,271 number of insertions = 6,007 mapped reads with insertion percentage = 0.5% number of deletions = 18,691 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.87% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2174X There is a 2.28% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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 9632821 0.03864712938869669 0.24914712362120917 chr2 243199373 5323278 0.021888535049800477 0.30774731690231627 chr3 198022430 5173320 0.026124919283133735 0.1773942472833772 chr4 191154276 3406696 0.017821709622650554 0.14957599007704034 chr5 180915260 3585633 0.019819406057841667 0.15395523152736057 chr6 171115067 4751300 0.027766695728786994 0.2102354925032215 chr7 159138663 4895112 0.03076004226578176 0.4075199148876624 chr8 146364022 9504456 0.0649371059234762 0.3136882316793853 chr9 141213431 2488633 0.01762320327731432 0.1618147782465533 chr10 135534747 3832007 0.028273244203569435 0.1955348535259526 chr11 135006516 3392433 0.025127920492370902 0.18000618338566088 chr12 133851895 2583571 0.019301714032513323 0.1523216744246997 chr13 115169878 1646800 0.014298877697864714 0.13202930170527669 chr14 107349540 1593713 0.014846016107754165 0.13659405267521 chr15 102531392 1466458 0.014302526976323504 0.13661272843942626 chr16 90354753 1898247 0.02100882285628073 0.16178165735694278 chr17 81195210 1269865 0.015639654112600977 0.1377871003564017 chr18 78077248 2574429 0.03297284504699756 0.2374007257202085 chr19 59128983 1343629 0.022723695416848284 0.1831979827877028 chr20 63025520 1973789 0.0313172981357393 0.19688507344340161 chr21 48129895 1153306 0.02396236268539543 0.17209597749553013 chr22 51304566 817476 0.015933786478185975 0.13800053856138672 chrMT 16571 5766 0.3479572747571058 0.6495556454877671 chrX 155270560 5199020 0.03348361724205799 0.20599387109962786 chrY 59373566 153976 0.0025933426333193464 0.058249421918371194