BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617506.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 = 4,014,434 number of mapped reads = 3,731,959 (92.96%) number of supplementary alignments = 20,208 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,890,018 number of mapped paired reads (second in pair) = 1,841,941 number of mapped paired reads (both in pair) = 3,632,488 number of mapped paired reads (singletons) = 99,471 number of mapped bases = 359,361,460 bp number of sequenced bases = 359,150,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 271,452 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 47,749.7499 std insert size = 2,070,680.7891 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 52.535 >>>>>>> ACTG content number of A's = 106,260,784 bp (29.59%) number of C's = 72,307,452 bp (20.13%) number of T's = 105,936,063 bp (29.5%) number of G's = 74,296,457 bp (20.69%) number of N's = 349,828 bp (0.1%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 5,470,921 number of insertions = 54,390 mapped reads with insertion percentage = 1.43% number of deletions = 123,883 mapped reads with deletion percentage = 3.25% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.1161X std coverageData = 1.2062X There is a 8.74% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 23040503 0.09243909968031734 1.1941148944983984 chr2 243199373 37195223 0.15294127834778587 1.3946910884277022 chr3 198022430 29809725 0.15053711339669956 0.47117108357421583 chr4 191154276 18580751 0.09720290536425144 0.7545731139203733 chr5 180915260 23077849 0.1275616495811354 0.4403075329145681 chr6 171115067 16977916 0.09921929317889933 0.7398205968368432 chr7 159138663 27685131 0.17396860372014059 1.6490399612298254 chr8 146364022 16029575 0.10951854684616415 0.5748966580011818 chr9 141213431 14878199 0.10535965945052352 2.147419809239372 chr10 135534747 15242031 0.11245847531629656 2.2825112893761457 chr11 135006516 20210837 0.14970267805444296 1.549578895115576 chr12 133851895 15646569 0.1168946394072344 0.4226794892832366 chr13 115169878 15253917 0.13244710565726223 0.446228992233668 chr14 107349540 10441553 0.09726686299727041 0.41553421399034585 chr15 102531392 8085727 0.07886098922757237 0.3415982980386653 chr16 90354753 9714191 0.107511676779195 1.8526404631998898 chr17 81195210 10010273 0.12328649682659852 1.6600043329469847 chr18 78077248 6440391 0.082487423224753 2.0781203996579847 chr19 59128983 4269500 0.07220655224190141 0.8040637721626939 chr20 63025520 10570519 0.1677180767409773 0.5308521874724976 chr21 48129895 5151479 0.10703283271239217 0.5580121852461175 chr22 51304566 2696765 0.052563840029365025 0.27686592792242715 chrMT 16571 249632 15.064389596282663 11.95977055989731 chrX 155270560 16876240 0.10868924540492415 0.5951543437719198 chrY 59373566 1226964 0.020665155938250364 1.5588149526795854