BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094114.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 = 389,032 number of mapped reads = 371,947 (95.61%) number of supplementary alignments = 28,204 (7.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 186,751 number of mapped paired reads (second in pair) = 185,196 number of mapped paired reads (both in pair) = 369,138 number of mapped paired reads (singletons) = 2,809 number of mapped bases = 45,009,733 bp number of sequenced bases = 44,120,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 360,786 duplication rate = 55.35% >>>>>>> Insert size mean insert size = 1,803,953.8264 std insert size = 11,833,862.0971 median insert size = 137 >>>>>>> Mapping quality mean mapping quality = 40.6657 >>>>>>> ACTG content number of A's = 12,485,518 bp (28.3%) number of C's = 9,566,433 bp (21.68%) number of T's = 11,861,505 bp (26.88%) number of G's = 10,206,638 bp (23.13%) number of N's = 414 bp (0%) GC percentage = 44.82% >>>>>>> Mismatches and indels general error rate = 0.0362 number of mismatches = 1,534,766 number of insertions = 30,233 mapped reads with insertion percentage = 8.01% number of deletions = 122,630 mapped reads with deletion percentage = 32.01% homopolymer indels = 27.78% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 3.1801X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% 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 904591 0.003629242713100402 1.3626395880891027 chr2 243199373 1804239 0.007418765014661448 2.8373375196229897 chr3 198022430 718731 0.0036295433805150256 1.196357547726983 chr4 191154276 1953475 0.0102193633377053 2.8573941468355817 chr5 180915260 876271 0.004843543877945951 1.8057147058400305 chr6 171115067 1168221 0.006827107749664148 2.35676713843452 chr7 159138663 960167 0.006033524361078741 1.9041388157588663 chr8 146364022 788598 0.005387922449958365 1.6069846796991734 chr9 141213431 1071936 0.007590892682155708 3.426688649132461 chr10 135534747 569464 0.004201608905500816 1.2440696054083507 chr11 135006516 1447212 0.010719571490904928 2.922299253085177 chr12 133851895 1333740 0.009964296732593888 2.4822730956672654 chr13 115169878 1201048 0.010428490685732948 2.9253729651406215 chr14 107349540 264125 0.0024604204172649457 0.9096388699777507 chr15 102531392 639305 0.0062352123337991935 1.786291223978085 chr16 90354753 265371 0.0029369899334460024 0.9705434231760715 chr17 81195210 460823 0.005675494896804873 1.6188832909746609 chr18 78077248 260472 0.0033360806979262385 1.2986363814918112 chr19 59128983 86968 0.0014708184647789393 0.576324397143521 chr20 63025520 236104 0.0037461650455244164 1.4278630003989594 chr21 48129895 118926 0.002470938280667348 0.9448318495299196 chr22 51304566 62339 0.0012150770362232477 0.4060293550269962 chrMT 16571 13868 0.8368837125098063 5.292997059627338 chrX 155270560 27017385 0.17400198080048143 10.81453725524037 chrY 59373566 786354 0.013244176709884665 2.9222831480757483