BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068161.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 = 5,129,638 number of mapped reads = 4,845,861 (94.47%) number of supplementary alignments = 30,429 (0.59%) number of secondary alignments = 0 number of mapped bases = 313,333,020 bp number of sequenced bases = 313,200,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 453,977 duplication rate = 6.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.409 >>>>>>> ACTG content number of A's = 81,289,445 bp (25.95%) number of C's = 56,879,975 bp (18.16%) number of T's = 101,279,579 bp (32.34%) number of G's = 73,716,292 bp (23.54%) number of N's = 35,420 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,845,528 number of insertions = 20,662 mapped reads with insertion percentage = 0.42% number of deletions = 76,467 mapped reads with deletion percentage = 1.56% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.1012X std coverageData = 1.5134X There is a 7.89% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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% 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 33574636 0.13470231634849167 4.018774381641182 chr2 243199373 28708884 0.11804670236547032 1.5919452017350064 chr3 198022430 19636905 0.09916505418098344 0.4003499102357922 chr4 191154276 15615869 0.08169249114783077 0.4287844704250826 chr5 180915260 16257141 0.08986052917813567 0.39264165028161224 chr6 171115067 22315662 0.1304131914929502 0.659154479570495 chr7 159138663 30509915 0.19171906075395392 2.3931740573867426 chr8 146364022 11617219 0.0793720945984936 1.4308962771739198 chr9 141213431 10136319 0.07178013400155966 0.9274769343222079 chr10 135534747 16699230 0.12320995441855216 0.840647472203159 chr11 135006516 14935350 0.11062688263135388 0.7311129657475276 chr12 133851895 12555185 0.09379908293416392 0.4596797423112204 chr13 115169878 7277699 0.0631909933949917 0.3510555985887701 chr14 107349540 6471637 0.060285651899393326 0.47822896353398264 chr15 102531392 5111474 0.0498527709445318 0.38327384258739816 chr16 90354753 6684656 0.07398233936846688 0.4496853432373908 chr17 81195210 9205692 0.11337727927546465 0.504493721121377 chr18 78077248 7490817 0.09594109925595738 1.7191232241229295 chr19 59128983 7254998 0.12269783162007031 2.3451096513557754 chr20 63025520 4650211 0.07378298505113484 0.43153766503875196 chr21 48129895 4999874 0.1038829193373474 0.4388928336531284 chr22 51304566 3263965 0.06361938623552531 0.303948646450717 chrMT 16571 143806 8.678172711363224 5.539924985956262 chrX 155270560 17377415 0.11191699830283346 0.6176801996874931 chrY 59373566 838461 0.014121789484566246 0.4407288974891856