BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013164.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 = 3,970,354 number of mapped reads = 3,533,506 (89%) number of supplementary alignments = 21,698 (0.55%) number of secondary alignments = 0 number of mapped bases = 228,634,949 bp number of sequenced bases = 228,486,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 496,405 duplication rate = 10.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0697 >>>>>>> ACTG content number of A's = 62,094,435 bp (27.18%) number of C's = 41,680,011 bp (18.24%) number of T's = 72,671,019 bp (31.81%) number of G's = 51,672,613 bp (22.62%) number of N's = 368,893 bp (0.16%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,137,937 number of insertions = 14,757 mapped reads with insertion percentage = 0.41% number of deletions = 83,541 mapped reads with deletion percentage = 2.33% homopolymer indels = 46.78% >>>>>>> Coverage mean coverageData = 0.0739X std coverageData = 0.6188X There is a 3.94% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% 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 16701266 0.06700591530321603 0.8342640909973639 chr2 243199373 23243585 0.09557419788249208 0.7367389484835868 chr3 198022430 14464243 0.07304345775375042 0.4439007571031208 chr4 191154276 15072833 0.07885166534281451 0.4650887481170156 chr5 180915260 12578915 0.06952931997002354 0.4337276523143132 chr6 171115067 12033202 0.0703222820232423 0.5282065200279396 chr7 159138663 14419861 0.09061192753642777 1.1258736225551116 chr8 146364022 13056157 0.08920332211149541 0.7437374074935482 chr9 141213431 8101172 0.05736828248298846 0.5077504212419394 chr10 135534747 10741390 0.07925192792074198 0.6472474562962821 chr11 135006516 9532794 0.07060988078530965 0.5095500733017762 chr12 133851895 11198661 0.08366456821548922 0.4794948768145837 chr13 115169878 5937865 0.05155744803341721 0.3774150021778349 chr14 107349540 7621141 0.07099369964696635 0.4588669084634558 chr15 102531392 6201684 0.060485709586386965 0.40733025595813954 chr16 90354753 7167055 0.07932128374032521 0.49510118015550675 chr17 81195210 5767069 0.07102720714682553 0.47931496214780356 chr18 78077248 5733138 0.0734290481139909 0.8184913155294129 chr19 59128983 4118489 0.06965262703740398 0.6908824511115981 chr20 63025520 5011302 0.07951226741167705 0.47434490522374617 chr21 48129895 3750375 0.0779219443549586 0.48319744880180177 chr22 51304566 2251840 0.043891609959238326 0.3425801606589824 chrMT 16571 527222 31.81594351578058 23.662189520969648 chrX 155270560 12911215 0.08315301368140876 0.5015007075570539 chrY 59373566 492475 0.00829451611513447 0.16221890189693292