BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548923.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 = 7,952,109 number of mapped reads = 6,915,348 (86.96%) number of secondary alignments = 0 number of mapped bases = 273,999,797 bp number of sequenced bases = 273,970,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 230,633 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.25 >>>>>>> ACTG content number of A's = 80,836,064 bp (29.51%) number of C's = 56,112,750 bp (20.48%) number of T's = 81,131,520 bp (29.61%) number of G's = 55,887,532 bp (20.4%) number of N's = 2,352 bp (0%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 715,288 number of insertions = 8,293 mapped reads with insertion percentage = 0.12% number of deletions = 22,243 mapped reads with deletion percentage = 0.32% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0885X std coverageData = 1.0541X There is a 7.21% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.05% 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% 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 21621558 0.08674625528816636 0.9804433580046585 chr2 243199373 23114002 0.09504137167327319 0.49148688831508647 chr3 198022430 18740896 0.09464026878167286 0.36474692740377335 chr4 191154276 18259526 0.09552245642676599 0.3754253721726116 chr5 180915260 17153103 0.0948129140681665 0.3701354904367166 chr6 171115067 16051274 0.09380397811491376 0.3993726888826709 chr7 159138663 15230603 0.09570649088587604 0.7124926467844558 chr8 146364022 14461003 0.09880162353013229 4.2383052092060405 chr9 141213431 11435862 0.08098282096127245 0.4533491904113682 chr10 135534747 12555080 0.09263366242163716 0.4588487083826889 chr11 135006516 12412246 0.09193812541610955 0.5597440477216473 chr12 133851895 12399337 0.0926347512674363 0.36968317791034744 chr13 115169878 9027095 0.07838069429925071 0.32635424802450674 chr14 107349540 8419684 0.07843241806159579 0.3783708505421557 chr15 102531392 7913949 0.07718561940522567 0.32403681948064467 chr16 90354753 7367532 0.08154006021133166 0.3644346030973792 chr17 81195210 6905318 0.08504587893793242 0.3777615385300403 chr18 78077248 7338352 0.09398835368787588 0.8191028152105816 chr19 59128983 4996445 0.08450077688635368 0.8256478286474244 chr20 63025520 5510734 0.0874365495120072 0.3614394292277448 chr21 48129895 3502070 0.07276288468944302 0.3463682130085445 chr22 51304566 2937959 0.057265059020282914 0.3204397766787851 chrMT 16571 12252 0.7393639490676484 1.1416280895305284 chrX 155270560 15847582 0.10206430633083309 0.44541522192555205 chrY 59373566 786335 0.013243856702155972 0.19421776293768087