BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124866.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 = 4,370,902 number of mapped reads = 4,299,120 (98.36%) number of supplementary alignments = 20,578 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,154,860 number of mapped paired reads (second in pair) = 2,144,260 number of mapped paired reads (both in pair) = 4,274,496 number of mapped paired reads (singletons) = 24,624 number of mapped bases = 375,294,751 bp number of sequenced bases = 375,091,124 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 379,199 duplication rate = 5.29% >>>>>>> Insert size mean insert size = 36,322.9838 std insert size = 1,748,228.5805 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.5573 >>>>>>> ACTG content number of A's = 106,535,229 bp (28.4%) number of C's = 69,558,182 bp (18.54%) number of T's = 113,147,811 bp (30.17%) number of G's = 85,838,335 bp (22.88%) number of N's = 11,567 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 2,919,602 number of insertions = 53,726 mapped reads with insertion percentage = 1.22% number of deletions = 118,676 mapped reads with deletion percentage = 2.7% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.1212X std coverageData = 1.5019X There is a 8.54% of reference with a coverageData >= 1X There is a 2.11% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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% 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 30007615 0.12039133495278233 1.5064791002696896 chr2 243199373 35399778 0.14555867296582217 1.5664785549563671 chr3 198022430 30594196 0.1544986393713076 0.5176326346152664 chr4 191154276 24781900 0.1296434509265176 0.878232083077331 chr5 180915260 16924919 0.09355163848533286 0.4899317093916136 chr6 171115067 24016524 0.1403530642921117 3.195857731743645 chr7 159138663 20365150 0.1279711015292368 1.4309991497087444 chr8 146364022 24234832 0.16557916125043354 0.7028988321282826 chr9 141213431 20291443 0.14369343522288613 1.9648822015352982 chr10 135534747 18207350 0.13433713791489943 2.7567197423404552 chr11 135006516 14683404 0.10876070603881074 1.6599621301460652 chr12 133851895 15787188 0.11794519606913298 0.5401759155764756 chr13 115169878 8305497 0.07211518449294528 0.3279046396249228 chr14 107349540 8092617 0.07538567002709094 0.4419825640413857 chr15 102531392 13887328 0.1354446450897692 0.4901132200685819 chr16 90354753 13009635 0.14398395843105233 2.5605120495665736 chr17 81195210 7025418 0.08652503023269476 1.1525932260585434 chr18 78077248 7789888 0.09977154932509916 1.9456931231094512 chr19 59128983 3781126 0.06394708327724832 1.0871639877977244 chr20 63025520 9867510 0.15656372212399042 0.5644116819846191 chr21 48129895 5278386 0.10966959308762257 0.7411471814661084 chr22 51304566 5254292 0.10241373058296604 0.42854196462921224 chrMT 16571 127767 7.7102769899221535 4.645709086303394 chrX 155270560 15971312 0.10286117342527779 0.7641417854636898 chrY 59373566 1609676 0.027110987404731595 1.6946598824540458