BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548966.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 4,764,616 number of mapped reads = 4,160,207 (87.31%) number of secondary alignments = 0 number of mapped bases = 164,566,405 bp number of sequenced bases = 164,549,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,710 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2458 >>>>>>> ACTG content number of A's = 47,574,672 bp (28.91%) number of C's = 34,324,643 bp (20.86%) number of T's = 48,299,520 bp (29.35%) number of G's = 34,350,589 bp (20.88%) number of N's = 271 bp (0%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 482,942 number of insertions = 5,424 mapped reads with insertion percentage = 0.13% number of deletions = 12,812 mapped reads with deletion percentage = 0.31% homopolymer indels = 40.38% >>>>>>> Coverage mean coverageData = 0.0532X std coverageData = 0.5381X There is a 4.65% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.06% 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 13323994 0.05345621185032073 0.9175351459816283 chr2 243199373 13922395 0.05724683755660834 0.49866665793902454 chr3 198022430 11226519 0.05669316854661363 0.26338545286070536 chr4 191154276 11101348 0.05807533178070262 0.2885735252081035 chr5 180915260 10531010 0.05820962808775777 0.2758237347148768 chr6 171115067 9707122 0.05672862226679314 0.2848378522959288 chr7 159138663 9438705 0.059311199566883376 0.8239007932542078 chr8 146364022 8727045 0.05962561619138889 1.1075306382604007 chr9 141213431 7063271 0.05001840795157792 0.496935445895192 chr10 135534747 7901343 0.05829754490927703 0.433428344852714 chr11 135006516 7565820 0.056040406227503864 0.39111606597071125 chr12 133851895 7747870 0.05788390220399943 0.28453268023319805 chr13 115169878 5364156 0.04657603266715278 0.23585031789045122 chr14 107349540 5128099 0.047770106886345295 0.32973519054734113 chr15 102531392 4661837 0.04546741158064059 0.23910086125017632 chr16 90354753 4588185 0.05077967508803881 0.2993363574910977 chr17 81195210 4316590 0.05316311146926032 0.2709148163467008 chr18 78077248 4506647 0.05772036176275065 0.9967659009848612 chr19 59128983 3379369 0.05715249660221621 0.8737452113265877 chr20 63025520 3314943 0.05259683696382037 0.26844507850083094 chr21 48129895 2144114 0.044548486964286954 0.29822891118980827 chr22 51304566 1773126 0.03456078353727814 0.20871506049782243 chrMT 16571 5783 0.34898316335767304 0.7413260559171907 chrX 155270560 5867529 0.03778906316818848 0.3106912373148885 chrY 59373566 1259585 0.021214575523390324 0.2078100704517075