BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472474.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,531,970 number of mapped reads = 17,341,860 (98.92%) number of supplementary alignments = 76,541 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,701,371 number of mapped paired reads (second in pair) = 8,640,489 number of mapped paired reads (both in pair) = 17,236,528 number of mapped paired reads (singletons) = 105,332 number of mapped bases = 1,705,426,275 bp number of sequenced bases = 1,705,219,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,968,991 duplication rate = 45.31% >>>>>>> Insert size mean insert size = 34,515.3989 std insert size = 1,831,215.0055 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 54.9943 >>>>>>> ACTG content number of A's = 477,051,281 bp (27.98%) number of C's = 378,967,429 bp (22.22%) number of T's = 472,901,114 bp (27.73%) number of G's = 376,037,002 bp (22.05%) number of N's = 262,576 bp (0.02%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 10,279,879 number of insertions = 92,433 mapped reads with insertion percentage = 0.52% number of deletions = 86,496 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 0.5509X std coverageData = 19.7579X There is a 5.83% of reference with a coverageData >= 1X There is a 2.64% of reference with a coverageData >= 2X There is a 1.12% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 168304631 0.6752425744207072 21.976952159864066 chr2 243199373 127504672 0.5242804306078536 17.172815990936403 chr3 198022430 219496666 1.108443452592719 27.901611969607448 chr4 191154276 80943461 0.42344572506450234 16.15076997736676 chr5 180915260 101660460 0.561923079346651 16.10178742222844 chr6 171115067 118871207 0.694685798767212 18.634361153005393 chr7 159138663 54669378 0.34353297287661644 10.628425663773482 chr8 146364022 52252662 0.35700482458728827 12.676039226673053 chr9 141213431 107429526 0.7607599733201016 23.944742458800413 chr10 135534747 73311660 0.5409067536017166 30.29610254866291 chr11 135006516 94278184 0.6983232127847815 32.81324999496546 chr12 133851895 72699412 0.5431332294548389 15.765762730466003 chr13 115169878 27523045 0.23897780806887717 8.810140791503317 chr14 107349540 35311415 0.32893867081312134 10.234120004275443 chr15 102531392 57736694 0.5631123587983669 17.14573450344271 chr16 90354753 43463310 0.48102959232260867 15.17280468319876 chr17 81195210 44822751 0.5520368873976679 14.25497560375109 chr18 78077248 34896454 0.44694779713547284 20.399597059947 chr19 59128983 27277778 0.46132668982316166 14.833361439257537 chr20 63025520 36165227 0.5738187800751188 16.489998802888834 chr21 48129895 15317704 0.3182575819041367 13.852251414693434 chr22 51304566 19821936 0.38635812648722145 13.8018370859296 chrMT 16571 1891 0.11411502021604007 0.41923148441416275 chrX 155270560 86542825 0.5573678938235297 26.544512519015743 chrY 59373566 5123326 0.08628967982148823 5.398527983457091