BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080986.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 = 3,578,993 number of mapped reads = 2,937,856 (82.09%) number of supplementary alignments = 18,510 (0.52%) number of secondary alignments = 0 number of mapped bases = 197,382,370 bp number of sequenced bases = 197,312,934 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,813 duplication rate = 6.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5451 >>>>>>> ACTG content number of A's = 55,772,385 bp (28.27%) number of C's = 34,275,304 bp (17.37%) number of T's = 65,056,065 bp (32.97%) number of G's = 41,815,218 bp (21.19%) number of N's = 393,962 bp (0.2%) GC percentage = 38.56% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,900,402 number of insertions = 14,701 mapped reads with insertion percentage = 0.5% number of deletions = 39,550 mapped reads with deletion percentage = 1.33% homopolymer indels = 49.58% >>>>>>> Coverage mean coverageData = 0.0638X std coverageData = 0.4484X There is a 4.53% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% 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 15933514 0.06392567423131916 0.5634494319180772 chr2 243199373 13162579 0.05412258608084487 0.3908284243950469 chr3 198022430 18036379 0.09108250514853292 0.4042437543953812 chr4 191154276 12435845 0.06505658811419944 0.35085683594688155 chr5 180915260 10933010 0.06043166286801898 0.32644143740776055 chr6 171115067 16528270 0.09659155263048812 0.5130278108159614 chr7 159138663 9797402 0.06156518984955906 0.39693089031926443 chr8 146364022 14479161 0.09892568407282494 0.9358225882234457 chr9 141213431 10175550 0.07205794751917047 0.507919352656722 chr10 135534747 8227095 0.060701002378379026 0.39989926607979115 chr11 135006516 8582181 0.06356864286461551 0.38308626546005087 chr12 133851895 8090514 0.06044377630962938 0.3321137881803365 chr13 115169878 5162464 0.04482477614502639 0.2787052041784467 chr14 107349540 5676391 0.05287764623863316 0.32901400758173494 chr15 102531392 5058593 0.04933701670606403 0.29354017564249557 chr16 90354753 4182216 0.04628661870173006 0.30922580161333274 chr17 81195210 3423096 0.04215884163610144 0.27857296888883015 chr18 78077248 4963648 0.06357355218257693 0.7463234108735263 chr19 59128983 3079655 0.05208367950451642 0.4513885191870297 chr20 63025520 3190436 0.050621335611352354 0.30926884940576443 chr21 48129895 3742625 0.07776092177221662 0.40488916021781274 chr22 51304566 1611721 0.031414767254828745 0.23035932365688278 chrMT 16571 32543 1.9638525134270715 1.995835918569886 chrX 155270560 10420509 0.06711194317841064 0.3671481319397823 chrY 59373566 456973 0.007696573252817592 0.15545827890500888