BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777281.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 11,526,294 number of mapped reads = 10,810,290 (93.79%) number of supplementary alignments = 1,084,432 (9.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,424,811 number of mapped paired reads (second in pair) = 5,385,479 number of mapped paired reads (both in pair) = 10,572,700 number of mapped paired reads (singletons) = 237,590 number of mapped bases = 975,182,466 bp number of sequenced bases = 970,896,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,879,491 duplication rate = 8.49% >>>>>>> Insert size mean insert size = 634,675.7142 std insert size = 7,858,513.8659 median insert size = 153 >>>>>>> Mapping quality mean mapping quality = 48.9833 >>>>>>> ACTG content number of A's = 275,013,287 bp (28.33%) number of C's = 211,179,973 bp (21.75%) number of T's = 269,587,017 bp (27.77%) number of G's = 215,099,291 bp (22.15%) number of N's = 17,036 bp (0%) GC percentage = 43.91% >>>>>>> Mismatches and indels general error rate = 0.0196 number of mismatches = 15,397,896 number of insertions = 1,069,233 mapped reads with insertion percentage = 8.67% number of deletions = 1,043,156 mapped reads with deletion percentage = 8.61% homopolymer indels = 22.06% >>>>>>> Coverage mean coverageData = 0.315X std coverageData = 51.8271X There is a 13.62% of reference with a coverageData >= 1X There is a 5.36% of reference with a coverageData >= 2X There is a 1.6% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% 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 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% 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 71924192 0.28856173642191246 16.839491415690194 chr2 243199373 148149723 0.609169839430466 127.03318887449602 chr3 198022430 44224858 0.22333256894181128 7.045484293962881 chr4 191154276 50637419 0.2649034071306885 26.782154116531835 chr5 180915260 56461366 0.3120873606792484 24.98578587580717 chr6 171115067 41508687 0.24257762760306784 22.873595693591394 chr7 159138663 46667032 0.2932476063343576 23.189952899119127 chr8 146364022 41576819 0.2840644745332292 9.507935525209454 chr9 141213431 42674908 0.3022014811041593 24.089041247638807 chr10 135534747 61542742 0.454073537319548 121.2306262226273 chr11 135006516 48153286 0.3566737919523825 16.150077639390542 chr12 133851895 40654944 0.30373080635130345 8.988025296348848 chr13 115169878 30467202 0.2645414107324139 8.770859490575116 chr14 107349540 17240174 0.16059848975598778 23.651067561372464 chr15 102531392 28265619 0.2756777065896072 5.183624146006831 chr16 90354753 50227518 0.5558923723691658 81.4457627203454 chr17 81195210 25221148 0.310623594667715 9.298285151487049 chr18 78077248 16852337 0.21584184165917322 15.81773424695883 chr19 59128983 17927922 0.3032002427641957 24.63620013539229 chr20 63025520 26279469 0.4169655244415278 19.152925771478454 chr21 48129895 7466289 0.15512788881006284 5.452305407630112 chr22 51304566 10449692 0.20367957113212887 13.806425526631099 chrMT 16571 2226179 134.34186228954198 28.45481406168967 chrX 155270560 24807192 0.15976751806652853 12.262974731459911 chrY 59373566 23575749 0.39707483630004636 127.17463380723963