BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124948.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,903,298 number of mapped reads = 4,356,824 (88.85%) number of supplementary alignments = 16,858 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,228,270 number of mapped paired reads (second in pair) = 2,128,554 number of mapped paired reads (both in pair) = 4,158,436 number of mapped paired reads (singletons) = 198,388 number of mapped bases = 288,810,051 bp number of sequenced bases = 288,682,710 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 251,674 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 92,971.714 std insert size = 2,856,307.0995 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 51.22 >>>>>>> ACTG content number of A's = 82,416,801 bp (28.55%) number of C's = 54,279,166 bp (18.8%) number of T's = 85,953,780 bp (29.77%) number of G's = 66,030,681 bp (22.87%) number of N's = 2,282 bp (0%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,769,855 number of insertions = 32,774 mapped reads with insertion percentage = 0.74% number of deletions = 80,720 mapped reads with deletion percentage = 1.83% homopolymer indels = 47.77% >>>>>>> Coverage mean coverageData = 0.0933X std coverageData = 1.8437X There is a 7.06% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.11% 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% 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 23875167 0.09578779344345144 1.1053211782915187 chr2 243199373 22760192 0.09358655706731613 2.2358373059425465 chr3 198022430 18978888 0.09584211243140486 0.39733598371963846 chr4 191154276 14318120 0.07490347744038957 4.999052600056992 chr5 180915260 10443500 0.057725920964323295 0.8164710242483769 chr6 171115067 15690325 0.09169458467383237 0.6158635557406423 chr7 159138663 17317770 0.10882188949897109 1.0888571467944717 chr8 146364022 16656766 0.11380369145636077 0.4831179872375122 chr9 141213431 9862254 0.06983934835490259 2.310715414467947 chr10 135534747 11733502 0.08657191059647605 2.584786487153214 chr11 135006516 17965900 0.13307431768700706 3.391189080496241 chr12 133851895 8433852 0.06300883525033396 0.30157676451807564 chr13 115169878 11890438 0.10324260307022293 0.4697123645533367 chr14 107349540 4824021 0.04493750974619919 0.5523151578714225 chr15 102531392 6261192 0.06106609768840357 0.2937824569031622 chr16 90354753 7969330 0.08820045139185982 1.2598139255094403 chr17 81195210 5882480 0.0724486087295051 0.7298437152399198 chr18 78077248 7794175 0.09982645648576138 1.3045939716176251 chr19 59128983 3691241 0.062426931983592546 0.7104430222435673 chr20 63025520 5159698 0.0818668057002941 0.3821952848325366 chr21 48129895 1814651 0.03770319881229743 0.30990749363442566 chr22 51304566 1390806 0.027108815227089144 0.20821127154795213 chrMT 16571 62576 3.776235592299801 2.975054912071602 chrX 155270560 43066729 0.27736570924971227 0.767456064905313 chrY 59373566 966478 0.01627791734793224 0.718777522078964