BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617409.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,762,935 (93.01%) number of supplementary alignments = 447,149 (1.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,002,900 number of mapped paired reads (second in pair) = 14,760,035 number of mapped paired reads (both in pair) = 29,219,894 number of mapped paired reads (singletons) = 543,041 number of mapped bases = 2,926,781,134 bp number of sequenced bases = 2,926,150,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,347,977 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 47,711.5437 std insert size = 2,073,353.6377 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.9089 >>>>>>> ACTG content number of A's = 874,213,825 bp (29.88%) number of C's = 586,921,361 bp (20.06%) number of T's = 864,165,052 bp (29.53%) number of G's = 598,386,755 bp (20.45%) number of N's = 2,463,254 bp (0.08%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 33,089,007 number of insertions = 235,271 mapped reads with insertion percentage = 0.78% number of deletions = 282,423 mapped reads with deletion percentage = 0.93% homopolymer indels = 44.71% >>>>>>> Coverage mean coverageData = 0.9454X std coverageData = 2.8868X There is a 29.47% of reference with a coverageData >= 1X There is a 16.89% of reference with a coverageData >= 2X There is a 10.79% of reference with a coverageData >= 3X There is a 7.46% of reference with a coverageData >= 4X There is a 5.41% of reference with a coverageData >= 5X There is a 4.07% of reference with a coverageData >= 6X There is a 3.15% of reference with a coverageData >= 7X There is a 2.49% of reference with a coverageData >= 8X There is a 2% of reference with a coverageData >= 9X There is a 1.63% of reference with a coverageData >= 10X There is a 1.35% of reference with a coverageData >= 11X There is a 1.13% of reference with a coverageData >= 12X There is a 0.96% of reference with a coverageData >= 13X There is a 0.82% of reference with a coverageData >= 14X There is a 0.7% of reference with a coverageData >= 15X There is a 0.61% of reference with a coverageData >= 16X There is a 0.53% of reference with a coverageData >= 17X There is a 0.46% of reference with a coverageData >= 18X There is a 0.41% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.32% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 188160087 0.7549031823675978 2.71432601600497 chr2 243199373 292305335 1.2019164827369846 3.0400836738211425 chr3 198022430 247446966 1.249590594358427 3.3763594884594053 chr4 191154276 141150528 0.7384115644894075 2.257452155648074 chr5 180915260 187630763 1.037119605057086 2.840637009283564 chr6 171115067 134197810 0.7842547845304587 2.571495219044173 chr7 159138663 219403528 1.3786940512375676 3.203396914284637 chr8 146364022 129522281 0.8849325075256541 3.2114276219366915 chr9 141213431 117340148 0.8309418386697226 2.5839856457873647 chr10 135534747 93779318 0.6919208548048568 2.370832785911061 chr11 135006516 217063697 1.6078016338115118 3.7870712114229677 chr12 133851895 139319292 1.0408466163291898 2.745529123261883 chr13 115169878 126969989 1.1024583094548386 2.7397131883403745 chr14 107349540 84712140 0.7891243874915533 2.8532406218772444 chr15 102531392 67056671 0.6540111247099815 2.3314641791710136 chr16 90354753 73376058 0.8120885239982892 3.2577016703886 chr17 81195210 89825902 1.106295580736844 3.603993445946171 chr18 78077248 41891400 0.5365378656788723 1.9749113001077787 chr19 59128983 41465591 0.7012735361945934 2.2846146791070727 chr20 63025520 99445895 1.5778671084348055 4.650940007011197 chr21 48129895 40150456 0.8342103385016735 2.4931564621402105 chr22 51304566 23444303 0.4569632847103706 2.048700113618803 chrMT 16571 179060 10.805624283386638 5.2515059338848715 chrX 155270560 128627281 0.8284074006044675 2.5322392821694817 chrY 59373566 2316635 0.03901795287148493 0.5553045697646862