BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094162.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 292,302 number of mapped reads = 267,369 (91.47%) number of supplementary alignments = 10,627 (3.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 134,556 number of mapped paired reads (second in pair) = 132,813 number of mapped paired reads (both in pair) = 264,450 number of mapped paired reads (singletons) = 2,919 number of mapped bases = 32,433,745 bp number of sequenced bases = 31,928,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 265,722 duplication rate = 51.42% >>>>>>> Insert size mean insert size = 151,058.1399 std insert size = 3,978,350.8954 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 33.0076 >>>>>>> ACTG content number of A's = 9,196,296 bp (28.8%) number of C's = 6,899,613 bp (21.61%) number of T's = 8,869,585 bp (27.78%) number of G's = 6,962,886 bp (21.81%) number of N's = 303 bp (0%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.031 number of mismatches = 951,494 number of insertions = 14,928 mapped reads with insertion percentage = 5.44% number of deletions = 75,897 mapped reads with deletion percentage = 27.32% homopolymer indels = 27.3% >>>>>>> Coverage mean coverageData = 0.0105X std coverageData = 10.4257X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 242749 9.739153267746523E-4 0.5828630132537493 chr2 243199373 991247 0.00407586165939663 2.25287531158358 chr3 198022430 136653 6.900884914905852E-4 0.17501420136205315 chr4 191154276 252578 0.001321330630343838 0.6246154528337482 chr5 180915260 1694329 0.009365318326381092 8.6421662527474 chr6 171115067 2073311 0.012116472478721 13.038121550073846 chr7 159138663 147652 9.278197844354141E-4 0.24908079512402842 chr8 146364022 189624 0.0012955642883330986 0.7105246681480076 chr9 141213431 202436 0.0014335463600484292 0.6419302274939607 chr10 135534747 55785 4.115918702382644E-4 0.11288453147176529 chr11 135006516 652036 0.004829663184553255 2.9611187679036126 chr12 133851895 163736 0.0012232624723019425 0.40516716793205404 chr13 115169878 5037188 0.04373702644714098 36.93923572512179 chr14 107349540 76878 7.161465247079773E-4 0.17247502870587023 chr15 102531392 384902 0.003753991753081827 2.7973408850383414 chr16 90354753 95243 0.0010541006071921862 0.5527386385228555 chr17 81195210 2700379 0.03325786090090783 13.137808620823156 chr18 78077248 257918 0.0033033695040071086 1.9998430982582305 chr19 59128983 1354749 0.022911758857750014 11.072069514434506 chr20 63025520 40801 6.473726833193919E-4 0.12547243000651354 chr21 48129895 33398 6.939138346343785E-4 0.14727472037830966 chr22 51304566 92082 0.0017948110115579186 0.2720719686491711 chrMT 16571 2551 0.15394363647335707 0.7929333642442457 chrX 155270560 15350949 0.09886580559766127 26.7825918505714 chrY 59373566 204571 0.003445489529801865 1.7980097851921304