BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004092.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,734,346 number of mapped reads = 2,478,216 (90.63%) number of supplementary alignments = 20,813 (0.76%) number of secondary alignments = 0 number of mapped bases = 163,687,495 bp number of sequenced bases = 163,591,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,635 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5159 >>>>>>> ACTG content number of A's = 45,933,574 bp (28.08%) number of C's = 29,319,086 bp (17.92%) number of T's = 52,211,751 bp (31.92%) number of G's = 36,054,687 bp (22.04%) number of N's = 72,421 bp (0.04%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,384,197 number of insertions = 11,988 mapped reads with insertion percentage = 0.48% number of deletions = 57,497 mapped reads with deletion percentage = 2.29% homopolymer indels = 44.55% >>>>>>> Coverage mean coverageData = 0.0529X std coverageData = 0.4234X There is a 4.39% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 11789850 0.047301186062039945 0.7665804129955931 chr2 243199373 14036363 0.057715457185820954 0.5550036751994905 chr3 198022430 10172471 0.051370296789106165 0.2614602575540803 chr4 191154276 10370257 0.05425071945552502 0.2760744684226762 chr5 180915260 9654500 0.05336476314933301 0.27146721572706506 chr6 171115067 10846551 0.06338746897139105 0.3421848979806419 chr7 159138663 10742583 0.06750454476295305 0.527428183107978 chr8 146364022 10552428 0.07209714420118901 0.5464245588089127 chr9 141213431 5894479 0.04174163150245956 0.3940432289271726 chr10 135534747 5191632 0.03830480459745131 0.3427991271778463 chr11 135006516 6331179 0.04689535873957373 0.3075022196833826 chr12 133851895 9087735 0.06789395846805157 0.3093788028704964 chr13 115169878 4764300 0.04136758745198983 0.2343180919888695 chr14 107349540 5264660 0.049042222258241626 0.27655743785667586 chr15 102531392 4428240 0.04318911421781926 0.24698298213011782 chr16 90354753 4008365 0.04436252512360916 0.28443013040668086 chr17 81195210 3703947 0.045617801838310414 0.2653907577882956 chr18 78077248 5895342 0.07550652912356746 0.6912882010447765 chr19 59128983 1734687 0.02933733867873222 0.5128597528183175 chr20 63025520 3622317 0.057473813782099696 0.2905495014464419 chr21 48129895 1974841 0.0410314836548054 0.25394729154363943 chr22 51304566 938130 0.018285506985869445 0.15249985864131826 chrMT 16571 7394 0.4462011948584877 0.74411566051299 chrX 155270560 12273847 0.07904812734622713 0.38493037332968993 chrY 59373566 401397 0.00676053380388168 0.12177772647042455