BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818777.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,719,639 number of mapped reads = 1,675,766 (97.45%) number of supplementary alignments = 16,228 (0.94%) number of secondary alignments = 0 number of mapped bases = 113,613,486 bp number of sequenced bases = 113,566,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 889,962 duplication rate = 44.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8665 >>>>>>> ACTG content number of A's = 32,172,444 bp (28.33%) number of C's = 25,123,517 bp (22.12%) number of T's = 32,149,745 bp (28.31%) number of G's = 24,113,802 bp (21.23%) number of N's = 6,839 bp (0.01%) GC percentage = 43.36% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 586,932 number of insertions = 13,834 mapped reads with insertion percentage = 0.82% number of deletions = 29,570 mapped reads with deletion percentage = 1.75% homopolymer indels = 39.81% >>>>>>> Coverage mean coverageData = 0.0367X std coverageData = 0.5205X There is a 1.45% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 9376396 0.037618345592807974 0.6796150731674742 chr2 243199373 10119412 0.04160953161667896 0.8416975262446804 chr3 198022430 7729610 0.039034012460103636 0.40108386942255003 chr4 191154276 7426573 0.03885119995955518 0.43763391634633636 chr5 180915260 7069229 0.039074807730425834 0.4161763588291673 chr6 171115067 6739111 0.03938350443447508 0.4328582182711517 chr7 159138663 6262615 0.03935319602377205 0.47678094253954706 chr8 146364022 5926850 0.04049389951855791 0.44991833504368933 chr9 141213431 4814593 0.03409444105922191 0.43524237153244394 chr10 135534747 5451605 0.040222932647670046 0.5334943238273283 chr11 135006516 5479097 0.040583944851965516 0.4602722694110725 chr12 133851895 5177893 0.03868374818301975 0.43038603504571266 chr13 115169878 3627144 0.03149385987888257 0.3637841422167772 chr14 107349540 3546276 0.03303485045208391 0.4065509479403923 chr15 102531392 3244746 0.03164636641234716 0.36070599895933614 chr16 90354753 3266432 0.03615119173642144 0.5638394225054449 chr17 81195210 2997786 0.03692072475703924 0.40932615660278726 chr18 78077248 3095775 0.039650155189896036 0.5831463260474369 chr19 59128983 2213825 0.037440606749485274 0.6039989430015581 chr20 63025520 2446226 0.03881326167558792 0.4360984701322479 chr21 48129895 1552136 0.032248896449909144 0.3899758965287284 chr22 51304566 1352637 0.026364846356949984 0.372851622441124 chrMT 16571 53394 3.2221350552169454 4.280055622463927 chrX 155270560 3508111 0.022593536083079756 0.3211713787252136 chrY 59373566 1136014 0.019133329468538237 0.9631166383506564