BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818829.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 923,848 number of mapped reads = 899,118 (97.32%) number of supplementary alignments = 6,603 (0.71%) number of secondary alignments = 0 number of mapped bases = 60,952,722 bp number of sequenced bases = 60,928,223 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 300,003 duplication rate = 28.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.783 >>>>>>> ACTG content number of A's = 17,464,766 bp (28.66%) number of C's = 14,106,631 bp (23.15%) number of T's = 16,528,276 bp (27.13%) number of G's = 12,824,601 bp (21.05%) number of N's = 3,949 bp (0.01%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 315,805 number of insertions = 6,311 mapped reads with insertion percentage = 0.69% number of deletions = 15,187 mapped reads with deletion percentage = 1.67% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.2884X There is a 1.16% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 5102803 0.02047257888276234 0.35193699624218816 chr2 243199373 5382108 0.022130435344502306 0.4823198198475719 chr3 198022430 4072666 0.020566690349169033 0.2231039964667499 chr4 191154276 4000877 0.020930094182146364 0.2566310237086907 chr5 180915260 3704577 0.02047686303521328 0.23168609261404222 chr6 171115067 3553095 0.020764360861337827 0.246327393173484 chr7 159138663 3386092 0.021277620008658737 0.2570674233430463 chr8 146364022 3098067 0.02116686162122547 0.23612490545544865 chr9 141213431 2557508 0.01811094016970666 0.23215516800650737 chr10 135534747 2971417 0.021923654751058043 0.30510487977249234 chr11 135006516 2889090 0.02139963377767633 0.2508352618536272 chr12 133851895 2785206 0.02080811780811919 0.23718150689078185 chr13 115169878 1892610 0.0164332031332012 0.19829241511237 chr14 107349540 1855553 0.017285150919137612 0.2270641384521316 chr15 102531392 1763691 0.017201473281470713 0.20575709410441162 chr16 90354753 1892555 0.02094582672369211 0.35622286169717227 chr17 81195210 1689418 0.02080686779429476 0.23795227605506608 chr18 78077248 1680828 0.021527756716015402 0.3000586515437054 chr19 59128983 1238484 0.02094546425735075 0.2957369021472562 chr20 63025520 1333918 0.021164728192643235 0.23328183878481537 chr21 48129895 866427 0.01800184687708128 0.22340170087450112 chr22 51304566 776188 0.015129023798778455 0.21332037580348012 chrMT 16571 50293 3.035000905195824 3.9624714944773882 chrX 155270560 1853801 0.011939166059554368 0.1787810881078744 chrY 59373566 555450 0.00935517331062783 0.5244886796433318