BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004164.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 = 3,394,328 number of mapped reads = 2,642,755 (77.86%) number of supplementary alignments = 13,817 (0.41%) number of secondary alignments = 0 number of mapped bases = 169,656,663 bp number of sequenced bases = 169,555,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 172,759 duplication rate = 5.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9315 >>>>>>> ACTG content number of A's = 44,796,176 bp (26.42%) number of C's = 30,899,752 bp (18.22%) number of T's = 54,454,875 bp (32.12%) number of G's = 39,383,575 bp (23.23%) number of N's = 21,530 bp (0.01%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,807,613 number of insertions = 15,060 mapped reads with insertion percentage = 0.56% number of deletions = 61,259 mapped reads with deletion percentage = 2.29% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.0548X std coverageData = 0.473X There is a 4.08% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14593106 0.05854792233396281 0.7079900051516852 chr2 243199373 14169943 0.05826471847030625 0.6635675628058594 chr3 198022430 10903935 0.055064140966253165 0.30273719760842077 chr4 191154276 11324155 0.05924091909929339 0.3301092106092106 chr5 180915260 9555900 0.05281975660870178 0.2969671676897523 chr6 171115067 10193002 0.05956811506259703 0.3649971904836333 chr7 159138663 10324708 0.06487869010185161 0.7516522760129706 chr8 146364022 10209615 0.0697549497512442 0.5428233781639703 chr9 141213431 6079331 0.04305065712906586 0.44474107399131996 chr10 135534747 8001474 0.05903632962844576 0.4009531514855696 chr11 135006516 7141807 0.05289972078088438 0.48403316526142387 chr12 133851895 7442003 0.055598787002604635 0.30788846005764275 chr13 115169878 5087300 0.04417214021881659 0.27237163612803594 chr14 107349540 4425352 0.041223763045468105 0.29436319778978454 chr15 102531392 4613993 0.045000783759963 0.28279628671394885 chr16 90354753 5047200 0.05585981735792028 0.33586817990125084 chr17 81195210 4406675 0.05427259810030666 0.3429258470752669 chr18 78077248 4831762 0.061884378916633946 0.8485930915531001 chr19 59128983 3166989 0.05356068782715238 0.5082554098801924 chr20 63025520 3918330 0.06217053028677907 0.33904019147852316 chr21 48129895 2506228 0.05207216845164528 0.31551585344554256 chr22 51304566 1900230 0.03703822384931587 0.2462975327141062 chrMT 16571 111974 6.757226479995173 6.083354421104406 chrX 155270560 9245033 0.05954144172597819 0.36089051452453613 chrY 59373566 456618 0.007690594161044664 0.16034561398762784