BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328245.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 391,589,876 number of mapped reads = 372,185,300 (95.04%) number of supplementary alignments = 16,906,520 (4.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 187,443,820 number of mapped paired reads (second in pair) = 184,741,480 number of mapped paired reads (both in pair) = 368,607,222 number of mapped paired reads (singletons) = 3,578,078 number of mapped bases = 51,670,393,954 bp number of sequenced bases = 51,592,469,757 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,321,815 duplication rate = 32.4% >>>>>>> Insert size mean insert size = 154,441.9837 std insert size = 3,777,242.5835 median insert size = 244 >>>>>>> Mapping quality mean mapping quality = 53.7269 >>>>>>> ACTG content number of A's = 14,833,282,953 bp (28.75%) number of C's = 10,941,228,456 bp (21.21%) number of T's = 14,734,263,154 bp (28.56%) number of G's = 11,079,784,332 bp (21.48%) number of N's = 3,910,862 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 496,496,470 number of insertions = 7,646,819 mapped reads with insertion percentage = 1.94% number of deletions = 33,479,818 mapped reads with deletion percentage = 8.57% homopolymer indels = 48.25% >>>>>>> Coverage mean coverageData = 16.6911X std coverageData = 156.9291X There is a 91.58% of reference with a coverageData >= 1X There is a 91.38% of reference with a coverageData >= 2X There is a 91.07% of reference with a coverageData >= 3X There is a 90.56% of reference with a coverageData >= 4X There is a 89.72% of reference with a coverageData >= 5X There is a 88.48% of reference with a coverageData >= 6X There is a 86.73% of reference with a coverageData >= 7X There is a 84.42% of reference with a coverageData >= 8X There is a 81.51% of reference with a coverageData >= 9X There is a 78.02% of reference with a coverageData >= 10X There is a 74.01% of reference with a coverageData >= 11X There is a 69.56% of reference with a coverageData >= 12X There is a 64.76% of reference with a coverageData >= 13X There is a 59.75% of reference with a coverageData >= 14X There is a 54.65% of reference with a coverageData >= 15X There is a 49.55% of reference with a coverageData >= 16X There is a 44.58% of reference with a coverageData >= 17X There is a 39.8% of reference with a coverageData >= 18X There is a 35.3% of reference with a coverageData >= 19X There is a 31.11% of reference with a coverageData >= 20X There is a 27.26% of reference with a coverageData >= 21X There is a 23.77% of reference with a coverageData >= 22X There is a 20.64% of reference with a coverageData >= 23X There is a 17.86% of reference with a coverageData >= 24X There is a 15.4% of reference with a coverageData >= 25X There is a 13.25% of reference with a coverageData >= 26X There is a 11.38% of reference with a coverageData >= 27X There is a 9.76% of reference with a coverageData >= 28X There is a 8.37% of reference with a coverageData >= 29X There is a 7.17% of reference with a coverageData >= 30X There is a 6.15% of reference with a coverageData >= 31X There is a 5.28% of reference with a coverageData >= 32X There is a 4.53% of reference with a coverageData >= 33X There is a 3.89% of reference with a coverageData >= 34X There is a 3.35% of reference with a coverageData >= 35X There is a 2.89% of reference with a coverageData >= 36X There is a 2.5% of reference with a coverageData >= 37X There is a 2.16% of reference with a coverageData >= 38X There is a 1.88% of reference with a coverageData >= 39X There is a 1.63% of reference with a coverageData >= 40X There is a 1.42% of reference with a coverageData >= 41X There is a 1.24% of reference with a coverageData >= 42X There is a 1.09% of reference with a coverageData >= 43X There is a 0.96% of reference with a coverageData >= 44X There is a 0.85% of reference with a coverageData >= 45X There is a 0.75% of reference with a coverageData >= 46X There is a 0.67% of reference with a coverageData >= 47X There is a 0.6% of reference with a coverageData >= 48X There is a 0.54% of reference with a coverageData >= 49X There is a 0.48% of reference with a coverageData >= 50X There is a 0.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3968962322 15.923580475251855 332.8601161433285 chr2 243199373 4096241067 16.84313991631878 134.29626847369562 chr3 198022430 3171297539 16.014840031000528 17.18484456907841 chr4 191154276 3156821511 16.514522076398645 144.14059024652303 chr5 180915260 2896185055 16.008517219608784 11.461346590413227 chr6 171115067 2753803115 16.09328251030051 48.40703706943615 chr7 159138663 3134792053 19.69849434389178 78.66848878419948 chr8 146364022 3848104037 26.291324769689645 267.41570687675596 chr9 141213431 2580215934 18.27174593612133 177.63572082470137 chr10 135534747 2780810673 20.517326623260676 324.7654768061358 chr11 135006516 2192138599 16.237279976916078 67.02698595799524 chr12 133851895 2329005731 17.399871185985077 11.3415786113706 chr13 115169878 1515010811 13.154575113815785 9.710061231037182 chr14 107349540 1445260889 13.463130712996069 13.58064270603719 chr15 102531392 1361573238 13.279574298571895 10.146915600009638 chr16 90354753 1458724744 16.14441626551732 33.98916840266091 chr17 81195210 1369593610 16.867911419897798 61.57388861563405 chr18 78077248 1272700795 16.30053347935624 181.1913526307093 chr19 59128983 1023246709 17.30533246276196 188.914343956222 chr20 63025520 1448973888 22.99027263876601 42.38723743245402 chr21 48129895 632164044 13.134540268579435 67.21803026950697 chr22 51304566 613620766 11.960353899105199 12.418435842300209 chrMT 16571 167334066 10098.006517409933 1788.863999077394 chrX 155270560 2297518610 14.796872053530302 31.380485431661402 chrY 59373566 156294148 2.632386068911542 162.17316682640072