BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549024.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 = 7,379,615 number of mapped reads = 6,566,494 (88.98%) number of secondary alignments = 0 number of mapped bases = 259,684,800 bp number of sequenced bases = 259,660,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 267,421 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.144 >>>>>>> ACTG content number of A's = 73,042,336 bp (28.13%) number of C's = 55,614,725 bp (21.42%) number of T's = 74,443,798 bp (28.67%) number of G's = 56,557,222 bp (21.78%) number of N's = 2,740 bp (0%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 788,069 number of insertions = 8,681 mapped reads with insertion percentage = 0.13% number of deletions = 18,842 mapped reads with deletion percentage = 0.29% homopolymer indels = 39.66% >>>>>>> Coverage mean coverageData = 0.0839X std coverageData = 0.6447X There is a 6.73% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 20408950 0.08188124032798297 0.6143929202139129 chr2 243199373 21964714 0.09031566870034653 0.7659767051929324 chr3 198022430 17373939 0.08773722754538463 0.35434904099698394 chr4 191154276 16428162 0.08594190171293893 0.36421724062772554 chr5 180915260 15852943 0.08762634506342915 0.3655080592540944 chr6 171115067 15017334 0.08776161131386519 0.4258693377025222 chr7 159138663 14639710 0.09199342085713011 1.0388084367617152 chr8 146364022 13159014 0.08990606994934862 1.1773282636764242 chr9 141213431 11029148 0.0781026841561551 0.793051431112092 chr10 135534747 11946000 0.08813975946699483 0.46525221611791306 chr11 135006516 11876831 0.08797227979722105 0.8446219851208395 chr12 133851895 12041311 0.08995995910255884 0.37936670421091034 chr13 115169878 8104760 0.07037222006955673 0.31429517793071055 chr14 107349540 7927560 0.07384810405335691 0.4614107686353652 chr15 102531392 7434717 0.07251161673490203 0.3245483644819672 chr16 90354753 7415248 0.08206815639239255 0.4510659080651906 chr17 81195210 7227046 0.08900828016825131 0.4148295196844468 chr18 78077248 6907977 0.0884761845089622 1.4428051436805025 chr19 59128983 5630128 0.09521773780550226 0.7530476160209028 chr20 63025520 5414676 0.08591243673991107 0.36721121956641306 chr21 48129895 3241195 0.06734265678327368 0.3967995854863711 chr22 51304566 3034444 0.05914569085332483 0.34535280717210354 chrMT 16571 19682 1.1877376139038078 2.9191522776491317 chrX 155270560 14748021 0.09498272563710726 0.4946926974658441 chrY 59373566 841290 0.01416943695111727 0.17907049789953963