BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038390.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 15,422,782 number of mapped reads = 14,656,844 (95.03%) number of supplementary alignments = 247,692 (1.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,425,336 number of mapped paired reads (second in pair) = 7,231,508 number of mapped paired reads (both in pair) = 14,441,038 number of mapped paired reads (singletons) = 215,806 number of mapped bases = 2,109,619,090 bp number of sequenced bases = 2,108,197,477 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,437,433 duplication rate = 10.06% >>>>>>> Insert size mean insert size = 76,229.018 std insert size = 2,615,191.2072 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 53.7217 >>>>>>> ACTG content number of A's = 622,453,754 bp (29.53%) number of C's = 428,628,041 bp (20.33%) number of T's = 620,330,032 bp (29.42%) number of G's = 436,739,177 bp (20.72%) number of N's = 46,473 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0153 number of mismatches = 31,176,427 number of insertions = 367,064 mapped reads with insertion percentage = 2.36% number of deletions = 700,006 mapped reads with deletion percentage = 4.59% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.6815X std coverageData = 11.7769X There is a 28.04% of reference with a coverageData >= 1X There is a 15.33% of reference with a coverageData >= 2X There is a 7.78% of reference with a coverageData >= 3X There is a 4.55% of reference with a coverageData >= 4X There is a 2.56% of reference with a coverageData >= 5X There is a 1.54% of reference with a coverageData >= 6X There is a 0.93% of reference with a coverageData >= 7X There is a 0.59% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 129861587 0.5210080780500844 15.999784930402008 chr2 243199373 239895592 0.9864153391546778 16.81665862235933 chr3 198022430 119750025 0.6047296005811059 1.4038876423052948 chr4 191154276 126061098 0.6594730739897233 8.255439493331762 chr5 180915260 127760089 0.706187465888726 1.628547871197882 chr6 171115067 169659446 0.9914933206904568 18.231481155297953 chr7 159138663 116464911 0.7318454786816954 9.860520005174632 chr8 146364022 88479979 0.6045200028733837 3.4535991971331224 chr9 141213431 80006760 0.566566221310776 18.953614210062057 chr10 135534747 98471235 0.7265386712973316 23.984894836108747 chr11 135006516 90908189 0.6733614916779276 7.449384668472678 chr12 133851895 71012209 0.530528230474436 1.309260727829299 chr13 115169878 142140470 1.2341809548500173 2.2026532932064202 chr14 107349540 37643948 0.3506670638737716 1.2357129014565653 chr15 102531392 34854627 0.33994102996280395 0.9410828339987595 chr16 90354753 84193584 0.9318113458845934 17.28589958960255 chr17 81195210 52482952 0.6463799034450431 8.333365617338139 chr18 78077248 32509285 0.41637334604826237 15.262985239014778 chr19 59128983 26996576 0.45657095100045947 8.724611961415784 chr20 63025520 60377283 0.957981512885574 3.0510247454722013 chr21 48129895 18633809 0.38715665180653314 4.185957907404231 chr22 51304566 10411013 0.20292566162629658 0.8161058144833466 chrMT 16571 1258725 75.95950757347173 49.28543386922719 chrX 155270560 114717605 0.7388239277297641 2.4539901877408945 chrY 59373566 35068093 0.5906347784466912 15.102097344187122