BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618593.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 58,099,888 number of mapped reads = 53,850,682 (92.69%) number of supplementary alignments = 341,085 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,261,368 number of mapped paired reads (second in pair) = 26,589,314 number of mapped paired reads (both in pair) = 52,524,080 number of mapped paired reads (singletons) = 1,326,602 number of mapped bases = 5,059,710,848 bp number of sequenced bases = 5,055,754,135 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,084,319 duplication rate = 25.45% >>>>>>> Insert size mean insert size = 135,163.7023 std insert size = 3,666,588.0241 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.3179 >>>>>>> ACTG content number of A's = 1,377,380,633 bp (27.24%) number of C's = 1,095,058,411 bp (21.66%) number of T's = 1,394,483,029 bp (27.58%) number of G's = 1,188,592,734 bp (23.51%) number of N's = 239,328 bp (0%) GC percentage = 45.17% >>>>>>> Mismatches and indels general error rate = 0.0162 number of mismatches = 80,401,237 number of insertions = 966,563 mapped reads with insertion percentage = 1.77% number of deletions = 2,958,760 mapped reads with deletion percentage = 5.34% homopolymer indels = 53.23% >>>>>>> Coverage mean coverageData = 1.6344X std coverageData = 6.2476X There is a 28.24% of reference with a coverageData >= 1X There is a 19.95% of reference with a coverageData >= 2X There is a 15.19% of reference with a coverageData >= 3X There is a 12.11% of reference with a coverageData >= 4X There is a 9.88% of reference with a coverageData >= 5X There is a 8.23% of reference with a coverageData >= 6X There is a 6.96% of reference with a coverageData >= 7X There is a 5.95% of reference with a coverageData >= 8X There is a 5.14% of reference with a coverageData >= 9X There is a 4.48% of reference with a coverageData >= 10X There is a 3.93% of reference with a coverageData >= 11X There is a 3.47% of reference with a coverageData >= 12X There is a 3.08% of reference with a coverageData >= 13X There is a 2.75% of reference with a coverageData >= 14X There is a 2.47% of reference with a coverageData >= 15X There is a 2.22% of reference with a coverageData >= 16X There is a 2.01% of reference with a coverageData >= 17X There is a 1.82% of reference with a coverageData >= 18X There is a 1.65% of reference with a coverageData >= 19X There is a 1.51% of reference with a coverageData >= 20X There is a 1.38% of reference with a coverageData >= 21X There is a 1.26% of reference with a coverageData >= 22X There is a 1.16% of reference with a coverageData >= 23X There is a 1.07% of reference with a coverageData >= 24X There is a 0.99% of reference with a coverageData >= 25X There is a 0.91% of reference with a coverageData >= 26X There is a 0.84% of reference with a coverageData >= 27X There is a 0.78% of reference with a coverageData >= 28X There is a 0.72% of reference with a coverageData >= 29X There is a 0.67% of reference with a coverageData >= 30X There is a 0.63% of reference with a coverageData >= 31X There is a 0.58% of reference with a coverageData >= 32X There is a 0.55% of reference with a coverageData >= 33X There is a 0.51% of reference with a coverageData >= 34X There is a 0.48% of reference with a coverageData >= 35X There is a 0.45% of reference with a coverageData >= 36X There is a 0.42% of reference with a coverageData >= 37X There is a 0.39% of reference with a coverageData >= 38X There is a 0.37% of reference with a coverageData >= 39X There is a 0.35% of reference with a coverageData >= 40X There is a 0.33% of reference with a coverageData >= 41X There is a 0.31% of reference with a coverageData >= 42X There is a 0.29% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.23% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 441633310 1.7718443718541428 7.97970972214594 chr2 243199373 414526770 1.704473020989244 6.398458112308096 chr3 198022430 322467052 1.628437000798344 5.094798431551013 chr4 191154276 252623390 1.321568082526179 4.982598824877217 chr5 180915260 291096193 1.6090195652926127 5.036007478986672 chr6 171115067 270639712 1.5816240892451627 6.1611397195562905 chr7 159138663 251482259 1.5802712820328269 5.240890839583667 chr8 146364022 259576689 1.7735006557827442 5.535528509248176 chr9 141213431 207795081 1.4714965816530583 7.47981632628332 chr10 135534747 247558250 1.8265297680453854 5.883558679099512 chr11 135006516 271876847 2.013805370697811 7.854504547244781 chr12 133851895 231900653 1.7325167716153738 6.221698171719879 chr13 115169878 131198134 1.1391705563845436 4.0500663169325675 chr14 107349540 153572779 1.4305862791773492 4.970200322164441 chr15 102531392 159677801 1.5573552439432403 5.559624248957412 chr16 90354753 174299670 1.9290592272439724 7.69932552050864 chr17 81195210 160636358 1.978396976866 7.026579324565631 chr18 78077248 144459875 1.8502173001794326 8.357582873533085 chr19 59128983 105379549 1.7821978943896262 6.827202489015457 chr20 63025520 153050870 2.428395196104689 7.365732153176243 chr21 48129895 66221448 1.3758901406288129 8.297100511299794 chr22 51304566 85020644 1.657174996860903 6.354733586668609 chrMT 16571 16202 0.9777321827288636 3.996549588830514 chrX 155270560 256240011 1.6502807164474709 5.28224303978023 chrY 59373566 6761301 0.11387729347433839 2.4702864958869486