BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549088.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 = 7,863,682 number of mapped reads = 6,923,007 (88.04%) number of secondary alignments = 0 number of mapped bases = 275,051,683 bp number of sequenced bases = 275,027,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 229,228 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2927 >>>>>>> ACTG content number of A's = 82,593,229 bp (30.03%) number of C's = 55,043,291 bp (20.01%) number of T's = 83,608,138 bp (30.4%) number of G's = 53,715,000 bp (19.53%) number of N's = 67,448 bp (0.02%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,088,643 number of insertions = 6,303 mapped reads with insertion percentage = 0.09% number of deletions = 19,859 mapped reads with deletion percentage = 0.29% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 0.0888X std coverageData = 0.7442X There is a 7.68% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% 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 21733464 0.08719522508230781 1.8768617541746573 chr2 243199373 24183598 0.09943939288034266 0.5539102227291616 chr3 198022430 19956001 0.10077646759511032 0.3626590114111929 chr4 191154276 20075094 0.10502037631635297 0.36966032855171566 chr5 180915260 18609752 0.1028644681493424 0.36983567611344365 chr6 171115067 16987474 0.09927515032910574 0.4817835263768348 chr7 159138663 15460845 0.09715329203186783 0.7739033288447825 chr8 146364022 15142841 0.10346013175287025 0.6212866534554408 chr9 141213431 11538233 0.0817077590870234 0.522442651821275 chr10 135534747 13000474 0.0959198603144919 0.6514590961957 chr11 135006516 12813299 0.0949087449971674 0.5744422467046334 chr12 133851895 12703000 0.09490340050845003 0.3708552880367198 chr13 115169878 9872533 0.08572148526544415 0.3185095259434706 chr14 107349540 8485979 0.07904998009306793 0.39581232054945115 chr15 102531392 7271629 0.07092100144314827 0.293775213005248 chr16 90354753 6861642 0.07594112951645167 0.40293656688011575 chr17 81195210 5818157 0.07165640682498389 0.3616032486092179 chr18 78077248 7741808 0.0991557489321345 1.1555163437667737 chr19 59128983 3786118 0.06403150887949485 1.419927098557126 chr20 63025520 5183718 0.08224792115955569 0.3394302980983897 chr21 48129895 3715693 0.07720135271435767 0.3694072909800559 chr22 51304566 2257524 0.04400239931861036 0.27901775741357954 chrMT 16571 16533 0.9977068372457908 1.5214137413553082 chrX 155270560 9480170 0.06105581122396931 0.3739680740331237 chrY 59373566 2356104 0.039682709979050275 0.36503595928627536