BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549086.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 = 7,328,873 number of mapped reads = 6,451,991 (88.04%) number of secondary alignments = 0 number of mapped bases = 256,151,680 bp number of sequenced bases = 256,126,413 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,174 duplication rate = 1.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0699 >>>>>>> ACTG content number of A's = 77,651,682 bp (30.32%) number of C's = 50,460,700 bp (19.7%) number of T's = 78,578,442 bp (30.68%) number of G's = 49,371,891 bp (19.28%) number of N's = 63,698 bp (0.02%) GC percentage = 38.98% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 1,046,170 number of insertions = 6,581 mapped reads with insertion percentage = 0.1% number of deletions = 20,231 mapped reads with deletion percentage = 0.31% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.0827X std coverageData = 0.7264X There is a 7.33% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% 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 20564284 0.08250444439213654 1.8849756328266085 chr2 243199373 22513873 0.09257372962059404 0.5138714227068509 chr3 198022430 18522875 0.09353927734348073 0.3423114563851802 chr4 191154276 18459753 0.09656991926249141 0.34201513669696554 chr5 180915260 16933084 0.09359677011215085 0.34686256333034504 chr6 171115067 15928723 0.09308778752954583 0.44590651830285744 chr7 159138663 14554181 0.09145597132483135 0.7316523514173469 chr8 146364022 13784382 0.094178759312859 0.4982991079495452 chr9 141213431 10863867 0.07693225016252173 0.5034072753219246 chr10 135534747 12101189 0.08928477211825245 0.6632916532292084 chr11 135006516 11777791 0.08723868557573917 0.54868772348176 chr12 133851895 11808252 0.08821878838547635 0.3503950122457284 chr13 115169878 9125685 0.07923673410507563 0.29956155012703384 chr14 107349540 8021905 0.07472696203449032 0.37546448104693286 chr15 102531392 7112425 0.069368267232732 0.28405438246687165 chr16 90354753 6442015 0.07129691340089214 0.3942020687101016 chr17 81195210 5609663 0.06908859525087749 0.33962561297975563 chr18 78077248 7276642 0.09319798259282909 1.0678386446597725 chr19 59128983 3800295 0.06427127285446461 1.4315922982637905 chr20 63025520 4826395 0.0765784241050292 0.3158430004297595 chr21 48129895 3346561 0.06953185748691121 0.3424038217888639 chr22 51304566 2179458 0.04248078036563061 0.27507603856416457 chrMT 16571 7918 0.47782270231126667 0.8705489277943534 chrX 155270560 8632077 0.05559377772579683 0.35762737309631043 chrY 59373566 1958387 0.03298415661946261 0.2779893301059447