BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708536.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 24,281,356 number of mapped reads = 23,711,124 (97.65%) number of supplementary alignments = 700 (0%) number of secondary alignments = 0 number of mapped bases = 1,182,779,793 bp number of sequenced bases = 1,182,675,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,075 duplication rate = 1.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6159 >>>>>>> ACTG content number of A's = 367,046,150 bp (31.04%) number of C's = 222,180,320 bp (18.79%) number of T's = 367,252,879 bp (31.05%) number of G's = 226,154,937 bp (19.12%) number of N's = 40,994 bp (0%) GC percentage = 37.91% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 2,229,136 number of insertions = 70,254 mapped reads with insertion percentage = 0.3% number of deletions = 62,947 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.15% >>>>>>> Coverage mean coverageData = 0.3821X std coverageData = 0.7838X There is a 25.95% of reference with a coverageData >= 1X There is a 8.14% of reference with a coverageData >= 2X There is a 2.66% of reference with a coverageData >= 3X There is a 0.91% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% 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 90421970 0.36277530478048436 0.778047649105798 chr2 243199373 103769190 0.4266836247147726 0.819717114079372 chr3 198022430 89551548 0.4522293156386375 0.8369735812591065 chr4 191154276 104520084 0.5467839181374107 0.9369019153389656 chr5 180915260 81873033 0.4525490718693382 0.8356448012128417 chr6 171115067 77772388 0.45450344825566996 0.8433805553721311 chr7 159138663 67204614 0.42230224090798096 0.8168137337455558 chr8 146364022 68414178 0.4674248293067541 0.8620673641820629 chr9 141213431 50748097 0.3593716025496187 0.759185855195658 chr10 135534747 56034003 0.41342905963442717 0.8032174440959001 chr11 135006516 54469983 0.4034618817953942 0.8014908349117822 chr12 133851895 54523893 0.40734494644248403 0.8030351316959736 chr13 115169878 47030481 0.4083574786803195 0.810584892626054 chr14 107349540 36560327 0.3405727402278575 0.7479780975090529 chr15 102531392 29853777 0.29116718711865336 0.6904927897841966 chr16 90354753 20860304 0.2308711308192055 0.5908504954772436 chr17 81195210 17781696 0.21899932274329975 0.5825820845493797 chr18 78077248 36959936 0.4733765206478589 0.8528436464415093 chr19 59128983 8604600 0.14552254348768354 0.4536789857317949 chr20 63025520 18590302 0.29496467462703996 0.6791242484331746 chr21 48129895 15765958 0.32757100342728773 0.7542553843983982 chr22 51304566 6182252 0.12050100959824901 0.4199844637596893 chrMT 16571 650 0.03922515237463038 0.2067743611050099 chrX 155270560 39534262 0.25461531149240396 0.6124662399560272 chrY 59373566 5752267 0.09688262618418439 0.3859879802001762