BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819119.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 5,658,912 number of mapped reads = 5,212,661 (92.11%) number of supplementary alignments = 24,228 (0.43%) number of secondary alignments = 0 number of mapped bases = 307,204,954 bp number of sequenced bases = 307,110,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 656,771 duplication rate = 8.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3396 >>>>>>> ACTG content number of A's = 73,738,014 bp (24.01%) number of C's = 60,846,147 bp (19.81%) number of T's = 95,051,421 bp (30.95%) number of G's = 77,470,662 bp (25.23%) number of N's = 4,520 bp (0%) GC percentage = 45.04% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,542,909 number of insertions = 16,661 mapped reads with insertion percentage = 0.32% number of deletions = 56,570 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 0.0992X std coverageData = 0.8382X There is a 6.72% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% 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 28661218 0.11498955503103842 1.6585515566281526 chr2 243199373 24706053 0.1015876508859256 1.0128777947620693 chr3 198022430 17528466 0.08851757853895642 0.41853749237405286 chr4 191154276 17518497 0.09164585468127326 0.5828489893261422 chr5 180915260 16385076 0.09056768345577924 0.42930379232142607 chr6 171115067 13709197 0.08011683155873117 0.5835174599710479 chr7 159138663 15394306 0.09673517239490695 1.0807997660790196 chr8 146364022 25304542 0.17288771963372254 0.939483399906658 chr9 141213431 13332031 0.09441050263837863 0.723575335847838 chr10 135534747 16458788 0.1214359296365529 0.8303990028827499 chr11 135006516 11050784 0.08185370845359789 0.8004167177366718 chr12 133851895 14939582 0.1116127791840377 0.47598945814769184 chr13 115169878 6702459 0.05819628462226903 0.343086159057228 chr14 107349540 7191214 0.06698877331006728 0.3841278001491758 chr15 102531392 8032646 0.0783432843669966 0.40116787766458045 chr16 90354753 9699991 0.10735451847231545 0.5164253397370847 chr17 81195210 10959124 0.13497254333106595 0.5964006443457668 chr18 78077248 7630941 0.09773578341285799 1.4556945422033638 chr19 59128983 6238684 0.10550974637936865 1.087265065023478 chr20 63025520 8933385 0.14174234500564215 0.5507775625202717 chr21 48129895 4280273 0.08893169203880458 0.54153135306702 chr22 51304566 2569034 0.050074178582857516 0.3121799061883529 chrMT 16571 73343 4.425985154788486 3.941703351301288 chrX 155270560 18844593 0.12136616883458139 0.5979264758060139 chrY 59373566 1060727 0.017865307264852512 0.5570313039584097