BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926951.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 9,841,840 number of mapped reads = 9,320,968 (94.71%) number of supplementary alignments = 491,875 (5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,652,606 number of mapped paired reads (second in pair) = 4,668,362 number of mapped paired reads (both in pair) = 9,087,952 number of mapped paired reads (singletons) = 233,016 number of mapped bases = 835,083,891 bp number of sequenced bases = 834,452,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 665,399 duplication rate = 5.98% >>>>>>> Insert size mean insert size = 547,584.0169 std insert size = 7,293,733.6751 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 52.1182 >>>>>>> ACTG content number of A's = 236,204,380 bp (28.31%) number of C's = 163,631,017 bp (19.61%) number of T's = 238,316,757 bp (28.56%) number of G's = 196,257,157 bp (23.52%) number of N's = 42,758 bp (0.01%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 8,348,275 number of insertions = 147,227 mapped reads with insertion percentage = 1.55% number of deletions = 420,477 mapped reads with deletion percentage = 4.4% homopolymer indels = 51.68% >>>>>>> Coverage mean coverageData = 0.2698X std coverageData = 1.1276X There is a 16.46% of reference with a coverageData >= 1X There is a 6.07% of reference with a coverageData >= 2X There is a 2.25% of reference with a coverageData >= 3X There is a 0.98% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% 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 71420289 0.28654006442776325 1.2252194623091648 chr2 243199373 74586533 0.3066888375571593 2.140713934634059 chr3 198022430 53953549 0.2724618064731354 0.7571508636942973 chr4 191154276 49259533 0.25769516659935976 1.1724635537847663 chr5 180915260 48513823 0.2681577164911351 0.7404255572466185 chr6 171115067 47005198 0.27469935186946454 0.7910678417881094 chr7 159138663 43558568 0.2737145529493358 0.8116799626458928 chr8 146364022 41834115 0.285822392882863 0.8060790077005461 chr9 141213431 35171664 0.24906741342471878 0.9341873628675185 chr10 135534747 39274871 0.289777137371275 1.9359596500919158 chr11 135006516 40871334 0.30273601016413165 1.0457052310446575 chr12 133851895 37442598 0.27973154956080376 1.0868355038678748 chr13 115169878 25691403 0.22307397946535987 0.6814600537441842 chr14 107349540 25452386 0.2370982306957254 0.7127016540412913 chr15 102531392 25081295 0.24462064262231026 0.7318744970152881 chr16 90354753 26365614 0.2918010743718153 1.0357726945785426 chr17 81195210 22072943 0.2718503098889701 0.8107286632107005 chr18 78077248 21934293 0.2809306624126916 1.0160902846737787 chr19 59128983 14619557 0.24724857858624086 0.8735656630912614 chr20 63025520 20180183 0.32019066244911587 0.8668923359387066 chr21 48129895 10943772 0.22737992675861854 1.1429997959500042 chr22 51304566 11377939 0.22177244419141953 0.7086137068375148 chrMT 16571 166646 10.056484219419469 11.652928624994772 chrX 155270560 46776299 0.3012567160187997 0.8105338513448411 chrY 59373566 1529486 0.025760386364531315 0.8362839121665536