BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081034.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 = 3,817,652 number of mapped reads = 2,180,088 (57.11%) number of supplementary alignments = 11,411 (0.3%) number of secondary alignments = 0 number of mapped bases = 134,948,923 bp number of sequenced bases = 134,905,533 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,592 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4517 >>>>>>> ACTG content number of A's = 38,103,062 bp (28.24%) number of C's = 27,395,962 bp (20.31%) number of T's = 39,311,582 bp (29.14%) number of G's = 30,093,218 bp (22.31%) number of N's = 1,709 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,012,836 number of insertions = 8,585 mapped reads with insertion percentage = 0.39% number of deletions = 25,079 mapped reads with deletion percentage = 1.14% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.3072X There is a 3.6% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 10373415 0.04161841185543125 0.4152745259967999 chr2 243199373 12341331 0.050745735269638215 0.35876088081752755 chr3 198022430 8658229 0.04372347617388596 0.2446149890294581 chr4 191154276 8802223 0.04604774313288184 0.26225877373816714 chr5 180915260 7645222 0.0422585800667119 0.24251346646579705 chr6 171115067 8206136 0.047956828956505625 0.2872545966385493 chr7 159138663 7221980 0.04538168075472646 0.43318569009924507 chr8 146364022 6945672 0.04745477683033335 0.3205033631435793 chr9 141213431 5777346 0.040912156578080734 0.29748043510122674 chr10 135534747 6363846 0.04695361256696779 0.30317240273586227 chr11 135006516 6227431 0.04612689212719184 0.2904566499508813 chr12 133851895 6082089 0.045438945784069776 0.25351263764239274 chr13 115169878 4600713 0.03994719001091587 0.2361655657327097 chr14 107349540 4028801 0.03752974628489326 0.23893855368439706 chr15 102531392 4062996 0.03962684911173351 0.24401168216937627 chr16 90354753 3657746 0.04048205410953865 0.250277142790507 chr17 81195210 3628374 0.0446870449623814 0.2710180861682309 chr18 78077248 3752001 0.048054985237184586 0.4804856111872766 chr19 59128983 2401113 0.04060805510556473 0.3437044005983072 chr20 63025520 2913508 0.046227432950969705 0.2600819059996223 chr21 48129895 1858932 0.03862322990731644 0.24537820756626072 chr22 51304566 1648805 0.032137587909816835 0.20944781917185057 chrMT 16571 92118 5.558988594532617 4.680429753676926 chrX 155270560 7326531 0.0471855772272606 0.2757960155388531 chrY 59373566 332365 0.0055978615129837405 0.1178929064318503