BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124843.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 83,864,376 number of mapped reads = 80,621,588 (96.13%) number of supplementary alignments = 2,093,845 (2.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,891,353 number of mapped paired reads (second in pair) = 39,730,235 number of mapped paired reads (both in pair) = 79,180,760 number of mapped paired reads (singletons) = 1,440,828 number of mapped bases = 9,814,175,148 bp number of sequenced bases = 9,806,414,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,363,463 duplication rate = 32.53% >>>>>>> Insert size mean insert size = 110,975.9158 std insert size = 3,188,053.2872 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 53.0123 >>>>>>> ACTG content number of A's = 2,830,961,043 bp (28.87%) number of C's = 1,963,664,893 bp (20.02%) number of T's = 2,862,519,620 bp (29.19%) number of G's = 2,149,122,691 bp (21.92%) number of N's = 146,041 bp (0%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 112,119,582 number of insertions = 1,942,065 mapped reads with insertion percentage = 2.2% number of deletions = 3,269,672 mapped reads with deletion percentage = 3.85% homopolymer indels = 41.39% >>>>>>> Coverage mean coverageData = 3.1703X std coverageData = 50.3723X There is a 56.13% of reference with a coverageData >= 1X There is a 44.55% of reference with a coverageData >= 2X There is a 32.89% of reference with a coverageData >= 3X There is a 26.71% of reference with a coverageData >= 4X There is a 20.78% of reference with a coverageData >= 5X There is a 17.08% of reference with a coverageData >= 6X There is a 13.75% of reference with a coverageData >= 7X There is a 11.45% of reference with a coverageData >= 8X There is a 9.45% of reference with a coverageData >= 9X There is a 7.97% of reference with a coverageData >= 10X There is a 6.7% of reference with a coverageData >= 11X There is a 5.72% of reference with a coverageData >= 12X There is a 4.88% of reference with a coverageData >= 13X There is a 4.2% of reference with a coverageData >= 14X There is a 3.63% of reference with a coverageData >= 15X There is a 3.16% of reference with a coverageData >= 16X There is a 2.75% of reference with a coverageData >= 17X There is a 2.41% of reference with a coverageData >= 18X There is a 2.12% of reference with a coverageData >= 19X There is a 1.87% of reference with a coverageData >= 20X There is a 1.65% of reference with a coverageData >= 21X There is a 1.47% of reference with a coverageData >= 22X There is a 1.31% of reference with a coverageData >= 23X There is a 1.17% of reference with a coverageData >= 24X There is a 1.05% of reference with a coverageData >= 25X There is a 0.94% of reference with a coverageData >= 26X There is a 0.84% of reference with a coverageData >= 27X There is a 0.76% of reference with a coverageData >= 28X There is a 0.69% of reference with a coverageData >= 29X There is a 0.62% of reference with a coverageData >= 30X There is a 0.57% of reference with a coverageData >= 31X There is a 0.52% of reference with a coverageData >= 32X There is a 0.47% of reference with a coverageData >= 33X There is a 0.43% of reference with a coverageData >= 34X There is a 0.39% of reference with a coverageData >= 35X There is a 0.36% of reference with a coverageData >= 36X There is a 0.33% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.28% of reference with a coverageData >= 39X There is a 0.26% of reference with a coverageData >= 40X There is a 0.24% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 809746938 3.248725859744197 25.398979805006856 chr2 243199373 891831687 3.6670805356064795 66.67244072904523 chr3 198022430 670170298 3.3843150899622834 8.905168831291435 chr4 191154276 609808901 3.1901399945664832 42.90165038247241 chr5 180915260 578334907 3.1967171094356552 8.031047206553593 chr6 171115067 558659909 3.2648200932533897 12.769547312757693 chr7 159138663 571054731 3.5884097568420565 21.77487016614057 chr8 146364022 543221731 3.711443041651315 10.749609258799001 chr9 141213431 404333556 2.8632797400128323 38.71090339511359 chr10 135534747 572952981 4.227351241523327 186.61183238772645 chr11 135006516 410184999 3.038260753280975 14.646946523958178 chr12 133851895 444842089 3.323390296416797 6.275481270851884 chr13 115169878 275343735 2.3907617146212483 4.899203453613506 chr14 107349540 299550731 2.7904239831861415 8.539687619115096 chr15 102531392 269354582 2.627045012711814 5.686928154757226 chr16 90354753 354357719 3.921849235756308 71.92059860477642 chr17 81195210 230070493 2.833547607057116 27.9780396545036 chr18 78077248 232521346 2.9780935157960484 41.80713057977225 chr19 59128983 145197860 2.4556123348172587 15.047041149663873 chr20 63025520 203847312 3.2343614459666497 15.42203177968465 chr21 48129895 120624890 2.5062363007440593 23.363193902389842 chr22 51304566 92317819 1.799407464045208 7.932452369298963 chrMT 16571 3018032 182.12733087924687 98.36686857615098 chrX 155270560 356028624 2.292956398173614 8.83631324711115 chrY 59373566 166799278 2.8093188473806676 81.57802548085643