BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472524.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 = 18,066,932 number of mapped reads = 17,884,646 (98.99%) number of supplementary alignments = 71,679 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,966,117 number of mapped paired reads (second in pair) = 8,918,529 number of mapped paired reads (both in pair) = 17,789,546 number of mapped paired reads (singletons) = 95,100 number of mapped bases = 1,757,898,219 bp number of sequenced bases = 1,757,660,119 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,503,469 duplication rate = 47.75% >>>>>>> Insert size mean insert size = 28,328.1343 std insert size = 1,631,160.2504 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 55.0063 >>>>>>> ACTG content number of A's = 484,568,882 bp (27.57%) number of C's = 397,250,723 bp (22.6%) number of T's = 481,788,894 bp (27.41%) number of G's = 393,776,384 bp (22.4%) number of N's = 275,236 bp (0.02%) GC percentage = 45% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 10,169,227 number of insertions = 92,689 mapped reads with insertion percentage = 0.51% number of deletions = 87,256 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.97% >>>>>>> Coverage mean coverageData = 0.5679X std coverageData = 19.1601X There is a 5.42% of reference with a coverageData >= 1X There is a 2.54% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 197599622 0.7927748432771207 27.890510119465148 chr2 243199373 134459460 0.5528774944662378 21.094830608663155 chr3 198022430 220452492 1.113270309833083 25.350579325634907 chr4 191154276 55169551 0.28861269627052444 10.193681418703154 chr5 180915260 82514706 0.45609588710206095 15.082375389617011 chr6 171115067 94483314 0.552162446337937 17.898531580855654 chr7 159138663 89737404 0.5638944195478128 17.002847325142188 chr8 146364022 93840220 0.641142670976888 20.156450526412712 chr9 141213431 103060329 0.7298195948514274 18.54458925469753 chr10 135534747 44984710 0.3319053674110595 13.670658827331183 chr11 135006516 83904287 0.6214832401126476 20.315483733370936 chr12 133851895 96474700 0.7207570725838435 21.977668896977132 chr13 115169878 35394793 0.30732682550901025 12.355505891217444 chr14 107349540 38240532 0.35622446076620357 16.135481840274892 chr15 102531392 50167059 0.4892848718956239 16.159656480286202 chr16 90354753 49288371 0.5454983757190948 17.723352841683457 chr17 81195210 63131921 0.7775325785843771 18.722631673030627 chr18 78077248 29238816 0.3744857400711664 11.644047951386504 chr19 59128983 34326773 0.5805405616396278 18.175868680628323 chr20 63025520 54329669 0.8620265092616451 34.50485621307436 chr21 48129895 5150599 0.10701454885783565 2.5272267101619583 chr22 51304566 14952814 0.2914519148256707 10.653349804040419 chrMT 16571 2574 0.1553316034035363 0.6434181158582446 chrX 155270560 84807457 0.5461914802136348 18.09755864330536 chrY 59373566 2186046 0.03681850606716127 1.0742944263856533