BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975225.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 3,523,284 number of mapped reads = 3,478,122 (98.72%) number of supplementary alignments = 16,728 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,738,359 number of mapped paired reads (second in pair) = 1,739,763 number of mapped paired reads (both in pair) = 3,462,964 number of mapped paired reads (singletons) = 15,158 number of mapped bases = 315,783,602 bp number of sequenced bases = 315,594,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 171,787 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 50,792.3073 std insert size = 2,156,056.4393 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 52.5413 >>>>>>> ACTG content number of A's = 93,861,347 bp (29.74%) number of C's = 60,281,857 bp (19.1%) number of T's = 94,038,899 bp (29.8%) number of G's = 67,407,294 bp (21.36%) number of N's = 4,658 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,627,522 number of insertions = 56,885 mapped reads with insertion percentage = 1.58% number of deletions = 104,808 mapped reads with deletion percentage = 2.94% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.102X std coverageData = 1.1187X There is a 7.26% of reference with a coverageData >= 1X There is a 1.89% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 30764133 0.12342650492333176 1.0726232474150958 chr2 243199373 27390970 0.11262763411811921 1.6235875926301861 chr3 198022430 19278865 0.09735697617689067 0.40316957229026235 chr4 191154276 13831018 0.07235526345222851 0.7685660936455732 chr5 180915260 18717057 0.10345759113963078 0.4227434394403941 chr6 171115067 23081726 0.1348900853949933 0.651158102685276 chr7 159138663 20760072 0.13045272348429873 1.244607748104171 chr8 146364022 22172457 0.15148843750686217 0.597177291862126 chr9 141213431 12545322 0.08883943907573494 1.1234237470046151 chr10 135534747 15020411 0.11082332267163933 2.7394325695772164 chr11 135006516 13107805 0.09709016563319062 0.7870433076131296 chr12 133851895 14880925 0.11117455602701777 0.4247874713287335 chr13 115169878 6152549 0.05342151182968172 0.2830941275451621 chr14 107349540 8948527 0.08335878290675489 0.4129926849138648 chr15 102531392 5860224 0.05715541246138549 0.29277974262805606 chr16 90354753 10773169 0.11923190139206069 2.507494575784963 chr17 81195210 9454267 0.11643872834370401 1.3298939854777547 chr18 78077248 10831878 0.1387328354605941 1.2468645979507809 chr19 59128983 7699043 0.130207600560287 0.8105527803806515 chr20 63025520 5995372 0.09512610129991787 0.43196334725489804 chr21 48129895 3898411 0.08099770423351225 0.4776412610637824 chr22 51304566 2033536 0.039636550087959035 0.34969859983169144 chrMT 16571 110936 6.694586928972301 4.617187058770691 chrX 155270560 9810368 0.06318240882238076 0.43335126132962554 chrY 59373566 2664561 0.04487790071426736 1.4496681668307463