BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234024.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,545,310 number of mapped reads = 2,230,149 (87.62%) number of supplementary alignments = 14,586 (0.57%) number of secondary alignments = 0 number of mapped bases = 150,175,766 bp number of sequenced bases = 150,098,594 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,061 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4014 >>>>>>> ACTG content number of A's = 41,384,894 bp (27.57%) number of C's = 28,282,792 bp (18.84%) number of T's = 46,927,666 bp (31.26%) number of G's = 33,464,956 bp (22.3%) number of N's = 38,286 bp (0.03%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,127,287 number of insertions = 11,306 mapped reads with insertion percentage = 0.5% number of deletions = 43,315 mapped reads with deletion percentage = 1.92% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.0485X std coverageData = 0.4966X There is a 4.11% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 17718274 0.07108617795580136 1.239191957547406 chr2 243199373 2660191 0.010938313562181758 0.392656647401849 chr3 198022430 9839886 0.04969076482901457 0.25620963936139585 chr4 191154276 6480010 0.03389937246290007 0.22906309878834422 chr5 180915260 12618930 0.06975050086985476 0.30179950136951783 chr6 171115067 11122470 0.064999945329186 0.34865312834407486 chr7 159138663 10221593 0.06423073316884659 0.6597696580204698 chr8 146364022 11244276 0.07682404354807905 0.45974798924275734 chr9 141213431 7693929 0.05448439957527836 0.33241081458925936 chr10 135534747 6306976 0.04653401536950521 0.44185685516832957 chr11 135006516 6447308 0.04775553203669073 0.3713055432774194 chr12 133851895 6302303 0.047084152226608375 0.24801426625082534 chr13 115169878 4588098 0.03983765616214337 0.22652313176668581 chr14 107349540 5922729 0.055172374283112904 0.28266182255421485 chr15 102531392 2091628 0.020399879092639257 0.16418587700737977 chr16 90354753 2692237 0.029796296382991607 0.22786476260883443 chr17 81195210 4623837 0.05694716474038308 0.3125931692609129 chr18 78077248 3010442 0.03855722476284 0.5885573920428551 chr19 59128983 5368049 0.09078541059973921 0.7687061005428775 chr20 63025520 2986834 0.04739086642997947 0.2583525674928008 chr21 48129895 2065285 0.0429106483610654 0.25375289566585024 chr22 51304566 1322123 0.02577008447942041 0.18034635771862298 chrMT 16571 47085 2.841409691629956 2.356762375871408 chrX 155270560 6462302 0.04161962190385608 0.25992620975025804 chrY 59373566 338971 0.005709123147496312 0.12910154776022564