BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549148.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 = 16,931,689 number of mapped reads = 14,922,385 (88.13%) number of secondary alignments = 0 number of mapped bases = 590,286,438 bp number of sequenced bases = 590,222,269 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,300,588 duplication rate = 7.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9309 >>>>>>> ACTG content number of A's = 159,838,714 bp (27.08%) number of C's = 133,965,924 bp (22.7%) number of T's = 162,272,953 bp (27.49%) number of G's = 134,028,637 bp (22.71%) number of N's = 116,041 bp (0.02%) GC percentage = 45.41% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,982,001 number of insertions = 18,790 mapped reads with insertion percentage = 0.13% number of deletions = 50,948 mapped reads with deletion percentage = 0.34% homopolymer indels = 45.1% >>>>>>> Coverage mean coverageData = 0.1907X std coverageData = 0.981X There is a 10.88% of reference with a coverageData >= 1X There is a 4.07% of reference with a coverageData >= 2X There is a 1.85% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 49915162 0.20026093335189724 1.4430185747297448 chr2 243199373 48038401 0.1975268291501722 1.0050060686488642 chr3 198022430 37142766 0.18756847898493115 0.7188240679476908 chr4 191154276 32376269 0.16937245494837896 0.6850446796246271 chr5 180915260 33382228 0.18451858621544695 0.7263723505107718 chr6 171115067 32304649 0.18878903866484184 0.7645400934249419 chr7 159138663 33352832 0.20958346244243614 1.2792797091972794 chr8 146364022 28676537 0.19592613408778833 1.2906227110127328 chr9 141213431 25515189 0.18068528481543658 0.9525240708397753 chr10 135534747 29261055 0.21589338267625202 0.9097948720485138 chr11 135006516 27187577 0.20137973933050757 0.8678056239307382 chr12 133851895 27306370 0.20400435869809688 0.7652050860861297 chr13 115169878 17029690 0.14786583346037754 0.6374757489385287 chr14 107349540 18632037 0.1735641997161795 0.922201377581775 chr15 102531392 18962598 0.18494431442030945 0.7012333994953921 chr16 90354753 21380965 0.23663353935569942 0.8695921600021161 chr17 81195210 22106162 0.272259435008543 0.9009130592042176 chr18 78077248 14731485 0.18867833302731163 1.694336375675215 chr19 59128983 18242533 0.30852100060642 1.595626798823706 chr20 63025520 14628212 0.23209982242113988 0.826546308973853 chr21 48129895 7946207 0.16509919666352899 0.7746533630873188 chr22 51304566 10421348 0.20312710568490142 0.7778522868939712 chrMT 16571 347900 20.99450847866755 28.24641877841912 chrX 155270560 17601858 0.11336249447416175 0.6561800747791752 chrY 59373566 3796408 0.06394104743514985 0.42642544123430215