BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230334.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 = 3,026,904 number of mapped reads = 2,641,160 (87.26%) number of supplementary alignments = 33,158 (1.1%) number of secondary alignments = 0 number of mapped bases = 175,671,897 bp number of sequenced bases = 175,594,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 414,975 duplication rate = 10.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8674 >>>>>>> ACTG content number of A's = 49,280,417 bp (28.06%) number of C's = 32,464,219 bp (18.49%) number of T's = 55,655,542 bp (31.7%) number of G's = 38,116,644 bp (21.71%) number of N's = 77,184 bp (0.04%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,489,769 number of insertions = 14,346 mapped reads with insertion percentage = 0.54% number of deletions = 47,524 mapped reads with deletion percentage = 1.78% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.5957X There is a 2.47% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 19017374 0.07629820107850403 1.018939474463592 chr2 243199373 18378136 0.07556818824528795 0.6366166424308619 chr3 198022430 15929804 0.08044444258158027 0.5449727878757447 chr4 191154276 10658328 0.055757727334333866 0.4603081403432811 chr5 180915260 8366813 0.046247138024730475 0.40546486839492435 chr6 171115067 7466006 0.04363149388826175 0.44367419375573375 chr7 159138663 9062815 0.05694917142793891 0.6098002512172842 chr8 146364022 10383288 0.07094153233914274 0.9799986893511085 chr9 141213431 4974824 0.035229113581979325 0.4200958907911543 chr10 135534747 6914097 0.05101346446605312 0.5220220741725358 chr11 135006516 5645670 0.04181775937392533 0.4596095993333729 chr12 133851895 6487119 0.04846490219656584 0.41467511363470866 chr13 115169878 6305519 0.05474972370813834 0.4519567895462929 chr14 107349540 4582114 0.042684058077938666 0.4021766082424348 chr15 102531392 3424321 0.03339778123757454 0.3377856232270835 chr16 90354753 3578815 0.03960848634050275 0.3792029293650424 chr17 81195210 3859365 0.047531929531311023 0.42443692999635924 chr18 78077248 3555216 0.04553459671119556 0.7333988187531176 chr19 59128983 2152088 0.036396499496701984 0.6179916312828673 chr20 63025520 2877311 0.045653110041773554 0.409755119437866 chr21 48129895 1899371 0.039463435355510335 0.3845853403285674 chr22 51304566 1482946 0.028904756742314124 0.3078774674967797 chrMT 16571 431509 26.04000965542212 23.06437271097179 chrX 155270560 17713919 0.11408420888029257 0.6938012362989434 chrY 59373566 525129 0.00884449150317163 0.18309604012494135