BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238614.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 = 3,305,521 number of mapped reads = 2,959,413 (89.53%) number of supplementary alignments = 22,211 (0.67%) number of secondary alignments = 0 number of mapped bases = 185,217,443 bp number of sequenced bases = 185,137,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 627,848 duplication rate = 16.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.729 >>>>>>> ACTG content number of A's = 46,180,673 bp (24.94%) number of C's = 33,448,303 bp (18.07%) number of T's = 61,036,403 bp (32.97%) number of G's = 44,462,517 bp (24.02%) number of N's = 9,762 bp (0.01%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 991,335 number of insertions = 12,404 mapped reads with insertion percentage = 0.42% number of deletions = 46,296 mapped reads with deletion percentage = 1.55% homopolymer indels = 43.08% >>>>>>> Coverage mean coverageData = 0.0598X std coverageData = 0.7218X There is a 3.41% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% 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% 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 13726652 0.055071686260713466 0.7603184037106105 chr2 243199373 14907312 0.061296671188375146 1.7343993140369174 chr3 198022430 11491563 0.05803162298331558 0.4009735844843918 chr4 191154276 10437260 0.05460123737959176 0.38735746072827715 chr5 180915260 10494615 0.058008456555848305 0.3957233718734771 chr6 171115067 9589180 0.056039366773003106 0.6564510327337777 chr7 159138663 11984758 0.07531015891468185 0.7074874172318801 chr8 146364022 10226474 0.0698701351620414 0.5640795289562699 chr9 141213431 7558008 0.05352187781628222 0.46193353797999664 chr10 135534747 8057299 0.05944821662595497 0.5077410559182297 chr11 135006516 7604895 0.05632983670210407 0.4591414227531455 chr12 133851895 10136441 0.07572878217376003 0.45886867029549167 chr13 115169878 4903591 0.04257702695491264 0.465144584568795 chr14 107349540 4755474 0.04429896951584515 0.3517289022784677 chr15 102531392 5946388 0.057995779477957345 0.5124733329697411 chr16 90354753 5085718 0.05628611479907426 0.43548383024200876 chr17 81195210 4581714 0.05642837797943992 0.39903365630570103 chr18 78077248 6008718 0.07695862948448183 1.324786329289422 chr19 59128983 3786805 0.06404312754711171 0.6194988513330678 chr20 63025520 3785793 0.0600676202274888 0.4099985614347515 chr21 48129895 2720471 0.0565235182831793 0.41062773592912544 chr22 51304566 1956439 0.038133818342796236 0.3115302530018832 chrMT 16571 54078 3.26341198479271 3.1359827066892425 chrX 155270560 14886469 0.09587438211081353 0.5223929604061887 chrY 59373566 531328 0.00894889823528538 0.2859105914828462