BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124840.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 160,877,568 number of mapped reads = 157,528,767 (97.92%) number of supplementary alignments = 1,617,372 (1.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 79,435,893 number of mapped paired reads (second in pair) = 78,092,874 number of mapped paired reads (both in pair) = 155,729,998 number of mapped paired reads (singletons) = 1,798,769 number of mapped bases = 21,766,016,166 bp number of sequenced bases = 21,751,029,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,515,993 duplication rate = 29.14% >>>>>>> Insert size mean insert size = 44,644.1232 std insert size = 2,005,347.4426 median insert size = 265 >>>>>>> Mapping quality mean mapping quality = 53.81 >>>>>>> ACTG content number of A's = 6,209,801,704 bp (28.55%) number of C's = 4,383,244,351 bp (20.15%) number of T's = 6,310,276,696 bp (29.01%) number of G's = 4,847,656,169 bp (22.29%) number of N's = 50,570 bp (0%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0123 number of mismatches = 256,108,906 number of insertions = 3,658,659 mapped reads with insertion percentage = 2.16% number of deletions = 7,533,082 mapped reads with deletion percentage = 4.58% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 7.0311X std coverageData = 71.6544X There is a 59.09% of reference with a coverageData >= 1X There is a 51.41% of reference with a coverageData >= 2X There is a 44.96% of reference with a coverageData >= 3X There is a 40.08% of reference with a coverageData >= 4X There is a 35.83% of reference with a coverageData >= 5X There is a 32.29% of reference with a coverageData >= 6X There is a 29.19% of reference with a coverageData >= 7X There is a 26.5% of reference with a coverageData >= 8X There is a 24.12% of reference with a coverageData >= 9X There is a 22.02% of reference with a coverageData >= 10X There is a 20.16% of reference with a coverageData >= 11X There is a 18.49% of reference with a coverageData >= 12X There is a 16.99% of reference with a coverageData >= 13X There is a 15.65% of reference with a coverageData >= 14X There is a 14.43% of reference with a coverageData >= 15X There is a 13.33% of reference with a coverageData >= 16X There is a 12.33% of reference with a coverageData >= 17X There is a 11.42% of reference with a coverageData >= 18X There is a 10.59% of reference with a coverageData >= 19X There is a 9.84% of reference with a coverageData >= 20X There is a 9.15% of reference with a coverageData >= 21X There is a 8.52% of reference with a coverageData >= 22X There is a 7.93% of reference with a coverageData >= 23X There is a 7.4% of reference with a coverageData >= 24X There is a 6.91% of reference with a coverageData >= 25X There is a 6.46% of reference with a coverageData >= 26X There is a 6.04% of reference with a coverageData >= 27X There is a 5.65% of reference with a coverageData >= 28X There is a 5.29% of reference with a coverageData >= 29X There is a 4.96% of reference with a coverageData >= 30X There is a 4.65% of reference with a coverageData >= 31X There is a 4.37% of reference with a coverageData >= 32X There is a 4.11% of reference with a coverageData >= 33X There is a 3.86% of reference with a coverageData >= 34X There is a 3.63% of reference with a coverageData >= 35X There is a 3.42% of reference with a coverageData >= 36X There is a 3.22% of reference with a coverageData >= 37X There is a 3.04% of reference with a coverageData >= 38X There is a 2.86% of reference with a coverageData >= 39X There is a 2.7% of reference with a coverageData >= 40X There is a 2.55% of reference with a coverageData >= 41X There is a 2.41% of reference with a coverageData >= 42X There is a 2.28% of reference with a coverageData >= 43X There is a 2.15% of reference with a coverageData >= 44X There is a 2.04% of reference with a coverageData >= 45X There is a 1.93% of reference with a coverageData >= 46X There is a 1.83% of reference with a coverageData >= 47X There is a 1.73% of reference with a coverageData >= 48X There is a 1.64% of reference with a coverageData >= 49X There is a 1.55% of reference with a coverageData >= 50X There is a 1.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1930447161 7.745004418665019 81.84475498510176 chr2 243199373 1900414506 7.814224529271299 79.11040847765999 chr3 198022430 1357285708 6.854201859860017 12.2604897833185 chr4 191154276 1134823807 5.936690670733413 71.71432709416307 chr5 180915260 1330694129 7.3553448669835815 14.295022836091384 chr6 171115067 964116551 5.634317117147843 31.580400556033766 chr7 159138663 1587650030 9.976519847976855 92.36801048879593 chr8 146364022 1665058911 11.376148921351724 36.9979978544835 chr9 141213431 1077871920 7.632927777245211 128.96165703308887 chr10 135534747 1076918207 7.945698286506559 175.91051596692884 chr11 135006516 969373515 7.180197991332507 34.48673307622947 chr12 133851895 1240854239 9.270352421981027 15.492421063995081 chr13 115169878 644477663 5.595887346516074 10.680373143924733 chr14 107349540 517092054 4.816900510239727 11.962910098308441 chr15 102531392 435714999 4.249576549199683 9.086660752741965 chr16 90354753 711549047 7.875059400582945 68.56685521013917 chr17 81195210 546874388 6.735303572710754 124.02052019922895 chr18 78077248 407932946 5.224735200707894 90.62508334638837 chr19 59128983 260357592 4.403214443921689 44.091785551909034 chr20 63025520 405183144 6.428874271882247 23.868536261992578 chr21 48129895 230882541 4.797071362819304 34.937081148453366 chr22 51304566 157720657 3.07420312258367 9.141269088354708 chrMT 16571 5903051 356.2278076157142 162.33855479548595 chrX 155270560 1014001626 6.530546589128035 19.652933324963875 chrY 59373566 192817774 3.2475356794301358 96.2935371467901