BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818874.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 = 1,988,287 number of mapped reads = 1,957,249 (98.44%) number of supplementary alignments = 31,369 (1.58%) number of secondary alignments = 0 number of mapped bases = 181,147,670 bp number of sequenced bases = 181,032,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 546,735 duplication rate = 24.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3286 >>>>>>> ACTG content number of A's = 52,594,365 bp (29.05%) number of C's = 39,085,212 bp (21.59%) number of T's = 51,295,783 bp (28.34%) number of G's = 38,054,725 bp (21.02%) number of N's = 2,663 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,106,776 number of insertions = 24,596 mapped reads with insertion percentage = 1.22% number of deletions = 59,901 mapped reads with deletion percentage = 2.99% homopolymer indels = 41.64% >>>>>>> Coverage mean coverageData = 0.0585X std coverageData = 0.6895X There is a 3.67% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 17179826 0.06892591051959707 1.0407353960042094 chr2 243199373 13646214 0.05611122196437571 1.0013288700845588 chr3 198022430 11355169 0.057342842424466765 0.3463044468647209 chr4 191154276 9180418 0.048026223593345095 0.4070376306574702 chr5 180915260 7911328 0.04372946759715018 0.3266712751859398 chr6 171115067 8971590 0.052430158005899036 0.36455427877020274 chr7 159138663 16298466 0.1024167583964181 1.46913832503889 chr8 146364022 15978839 0.10917190428123108 0.6113556195348138 chr9 141213431 6743559 0.04775437401559913 0.5466988736995628 chr10 135534747 8413933 0.06207952710458817 0.8799580660286952 chr11 135006516 8058059 0.05968644506017769 0.42045877342314897 chr12 133851895 6967077 0.0520506414944667 0.3330575830411164 chr13 115169878 5487925 0.047650697346401635 0.31477585499157335 chr14 107349540 5317461 0.049534082772967634 0.3470020790420363 chr15 102531392 5014729 0.04890920626533579 0.3165948859299072 chr16 90354753 4541865 0.05026702911799227 0.7587835101274846 chr17 81195210 4436518 0.0546401444124598 0.4260155836530692 chr18 78077248 3505563 0.04489864960404342 0.6245360845521851 chr19 59128983 3073526 0.051980024753681284 0.8538034938153974 chr20 63025520 7336483 0.1164049578646872 0.5329511061966965 chr21 48129895 1772734 0.036832284799291584 0.3324341754856465 chr22 51304566 1619648 0.031569275919807994 0.28301000238985674 chrMT 16571 275798 16.643413191720477 10.870249178855698 chrX 155270560 7410144 0.04772407596134129 0.37500424292586465 chrY 59373566 650798 0.01096107314827612 0.8644685372583466