BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104288.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 157,308,262 number of mapped reads = 154,218,127 (98.04%) number of supplementary alignments = 151,510 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 77,736,841 number of mapped paired reads (second in pair) = 76,481,286 number of mapped paired reads (both in pair) = 152,683,450 number of mapped paired reads (singletons) = 1,534,677 number of mapped bases = 13,151,607,178 bp number of sequenced bases = 13,148,373,477 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,762,573 duplication rate = 30.2% >>>>>>> Insert size mean insert size = 10,457.5381 std insert size = 955,167.5312 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.071 >>>>>>> ACTG content number of A's = 4,099,029,063 bp (31.18%) number of C's = 2,474,157,830 bp (18.82%) number of T's = 4,148,749,673 bp (31.55%) number of G's = 2,419,496,150 bp (18.4%) number of N's = 6,940,761 bp (0.05%) GC percentage = 37.22% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 81,590,337 number of insertions = 1,287,405 mapped reads with insertion percentage = 0.82% number of deletions = 1,477,971 mapped reads with deletion percentage = 0.94% homopolymer indels = 44.97% >>>>>>> Coverage mean coverageData = 4.2484X std coverageData = 38.0928X There is a 68.47% of reference with a coverageData >= 1X There is a 57.21% of reference with a coverageData >= 2X There is a 47.48% of reference with a coverageData >= 3X There is a 40.23% of reference with a coverageData >= 4X There is a 33.73% of reference with a coverageData >= 5X There is a 28.41% of reference with a coverageData >= 6X There is a 23.71% of reference with a coverageData >= 7X There is a 19.79% of reference with a coverageData >= 8X There is a 16.39% of reference with a coverageData >= 9X There is a 13.56% of reference with a coverageData >= 10X There is a 11.15% of reference with a coverageData >= 11X There is a 9.15% of reference with a coverageData >= 12X There is a 7.49% of reference with a coverageData >= 13X There is a 6.12% of reference with a coverageData >= 14X There is a 4.99% of reference with a coverageData >= 15X There is a 4.07% of reference with a coverageData >= 16X There is a 3.31% of reference with a coverageData >= 17X There is a 2.7% of reference with a coverageData >= 18X There is a 2.2% of reference with a coverageData >= 19X There is a 1.8% of reference with a coverageData >= 20X There is a 1.47% of reference with a coverageData >= 21X There is a 1.21% of reference with a coverageData >= 22X There is a 1% of reference with a coverageData >= 23X There is a 0.82% of reference with a coverageData >= 24X There is a 0.68% of reference with a coverageData >= 25X There is a 0.57% of reference with a coverageData >= 26X There is a 0.48% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.34% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 892440560 3.5804948305424684 54.53082817062467 chr2 243199373 1253191050 5.152937010244677 18.953383053551473 chr3 198022430 1028010734 5.191385309229869 6.542341485509129 chr4 191154276 1337110399 6.994928007783619 14.752900842199413 chr5 180915260 1011496076 5.5909936840043235 6.291958762387479 chr6 171115067 854016247 4.990888657396838 15.078588449706723 chr7 159138663 753433798 4.734448460208567 32.88850558674801 chr8 146364022 803438935 5.489319875344775 112.92297839921046 chr9 141213431 525318430 3.7200316307023233 21.39565824878987 chr10 135534747 545371136 4.0238473754630615 47.770334660300875 chr11 135006516 617085002 4.570779398529179 14.961989596969957 chr12 133851895 520881176 3.8914740504794496 5.581266298040573 chr13 115169878 527797254 4.582771668821252 6.1496107812882785 chr14 107349540 298088918 2.7768066635404307 5.816863380897603 chr15 102531392 162559805 1.585463747532073 2.8605848598336747 chr16 90354753 211490310 2.3406661296500917 17.522542505656634 chr17 81195210 90199965 1.1109025396941519 6.354172258695535 chr18 78077248 370147637 4.740787444250084 22.61249187200318 chr19 59128983 46378214 0.7843567003342506 35.49238987822036 chr20 63025520 139927333 2.2201694329535084 5.300454139982105 chr21 48129895 123009244 2.555776280002273 6.695085467105484 chr22 51304566 18793972 0.36632162525261397 1.5598199543664832 chrMT 16571 121984342 7361.314465029268 1432.321439526211 chrX 155270560 879452745 5.66400188805914 10.054826450340377 chrY 59373566 19983896 0.3365790089145058 11.483065425575687