BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927048.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 21,666,820 number of mapped reads = 21,098,859 (97.38%) number of supplementary alignments = 644,764 (2.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,590,046 number of mapped paired reads (second in pair) = 10,508,813 number of mapped paired reads (both in pair) = 20,770,910 number of mapped paired reads (singletons) = 327,949 number of mapped bases = 1,878,092,305 bp number of sequenced bases = 1,876,719,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,902,428 duplication rate = 7.04% >>>>>>> Insert size mean insert size = 319,399.3628 std insert size = 5,513,679.9271 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 52.6342 >>>>>>> ACTG content number of A's = 538,212,793 bp (28.68%) number of C's = 356,056,458 bp (18.97%) number of T's = 555,863,489 bp (29.62%) number of G's = 426,374,614 bp (22.72%) number of N's = 211,669 bp (0.01%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 19,462,214 number of insertions = 317,552 mapped reads with insertion percentage = 1.48% number of deletions = 933,644 mapped reads with deletion percentage = 4.31% homopolymer indels = 51.41% >>>>>>> Coverage mean coverageData = 0.6067X std coverageData = 2.5113X There is a 29.42% of reference with a coverageData >= 1X There is a 13.92% of reference with a coverageData >= 2X There is a 6.82% of reference with a coverageData >= 3X There is a 3.7% of reference with a coverageData >= 4X There is a 2.12% of reference with a coverageData >= 5X There is a 1.27% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% 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 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% 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 157747870 0.6328885736256601 3.192195748784348 chr2 243199373 165269846 0.6795652635173529 3.9317557285837386 chr3 198022430 131067962 0.6618844239008682 1.4050935439260481 chr4 191154276 113400306 0.5932397034110815 2.0737599738290213 chr5 180915260 111459997 0.6160895272184337 1.2999949892146647 chr6 171115067 111677898 0.6526479518019299 1.4319987476380462 chr7 159138663 100310904 0.6303364758066367 2.0239172080123993 chr8 146364022 93688291 0.6401046494882465 1.6394685610496889 chr9 141213431 84268821 0.596747918404447 3.2210452769477667 chr10 135534747 91671705 0.6763705029825304 5.489560432452491 chr11 135006516 87493313 0.6480673347647902 2.017260807139744 chr12 133851895 80044834 0.5980104652235219 1.2964406884195054 chr13 115169878 59724144 0.5185743445868719 1.2075246223962504 chr14 107349540 59504885 0.5543096411964131 1.3494973149737697 chr15 102531392 51202777 0.4993863440379313 1.201407626529321 chr16 90354753 56370348 0.6238780598514834 3.2304810313552563 chr17 81195210 47512974 0.5851696670283875 1.7379334310392087 chr18 78077248 48420701 0.6201640329331279 3.2170639474164617 chr19 59128983 26474521 0.44774186290334134 1.9303276719892974 chr20 63025520 41871935 0.664364768430312 1.4823906271785607 chr21 48129895 22800253 0.473723306481346 1.7454965681624444 chr22 51304566 19323520 0.37664327966442596 1.101575703886079 chrMT 16571 153044 9.235652646189125 5.637415059572243 chrX 155270560 112026117 0.7214897466718739 1.6113546314307372 chrY 59373566 4605339 0.0775654775392807 2.830225104161607