BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506022.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,525,354 number of mapped reads = 3,994,452 (72.29%) number of supplementary alignments = 164 (0%) number of secondary alignments = 0 number of mapped bases = 185,195,116 bp number of sequenced bases = 185,158,373 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 298,379 duplication rate = 5.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9328 >>>>>>> ACTG content number of A's = 54,657,776 bp (29.52%) number of C's = 38,334,515 bp (20.7%) number of T's = 53,214,811 bp (28.74%) number of G's = 38,347,323 bp (20.71%) number of N's = 603,948 bp (0.33%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,474,456 number of insertions = 7,727 mapped reads with insertion percentage = 0.19% number of deletions = 26,604 mapped reads with deletion percentage = 0.66% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.0598X std coverageData = 0.5107X There is a 4.16% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% 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 18919601 0.07590593324941004 0.952177582280434 chr2 243199373 11415218 0.04693769502440288 0.40281555822567894 chr3 198022430 11217781 0.05664904223223601 0.32498732310412826 chr4 191154276 7726235 0.04041884472414313 0.2862694725907888 chr5 180915260 12863570 0.07110273616498686 0.3647999062794347 chr6 171115067 12290732 0.07182729268370038 0.4379382984817814 chr7 159138663 11592266 0.07284380666186695 0.714801547625237 chr8 146364022 11424737 0.07805700365353448 0.550433657251157 chr9 141213431 9215951 0.06526256698628051 0.4212580650745984 chr10 135534747 5900442 0.043534533620371164 0.5603795903167594 chr11 135006516 9282927 0.06875910344949572 0.49277581148764954 chr12 133851895 5067730 0.0378607265888914 0.2772485303143905 chr13 115169878 5922689 0.05142567746750587 0.3085636772942677 chr14 107349540 6481440 0.060376970409002216 0.7601666700890585 chr15 102531392 6472824 0.06313016797821296 0.33989450884697714 chr16 90354753 5839808 0.0646319956184264 0.37572586415606857 chr17 81195210 2975207 0.03664264185042443 0.2921467371780944 chr18 78077248 4912818 0.06292253026131249 0.5768034763613663 chr19 59128983 4258691 0.07202374848896015 0.7587946845981234 chr20 63025520 4346760 0.06896825286011127 0.36516381416003396 chr21 48129895 2474818 0.05141955950662265 0.3354497383852249 chr22 51304566 1488182 0.02900681393543023 0.23054407392798643 chrMT 16571 10794 0.6513789149719389 1.2168064232079503 chrX 155270560 12437644 0.08010304078248962 0.4230514523124879 chrY 59373566 656251 0.011052915366410702 0.20910442425319928