BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238637.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 = 3,840,315 number of mapped reads = 3,499,229 (91.12%) number of supplementary alignments = 30,903 (0.8%) number of secondary alignments = 0 number of mapped bases = 215,470,244 bp number of sequenced bases = 215,382,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 756,751 duplication rate = 16.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9693 >>>>>>> ACTG content number of A's = 55,910,848 bp (25.96%) number of C's = 39,595,092 bp (18.38%) number of T's = 69,698,411 bp (32.36%) number of G's = 50,167,285 bp (23.29%) number of N's = 11,042 bp (0.01%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,194,406 number of insertions = 13,895 mapped reads with insertion percentage = 0.39% number of deletions = 51,371 mapped reads with deletion percentage = 1.46% homopolymer indels = 42.05% >>>>>>> Coverage mean coverageData = 0.0696X std coverageData = 0.784X There is a 3.76% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% 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 0.02% 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% 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 13304367 0.053377467813811384 0.6610314991015508 chr2 243199373 20614755 0.08476483613302736 1.6276098264705645 chr3 198022430 16250735 0.08206512262272511 0.48389692811936147 chr4 191154276 8949178 0.046816520076171354 0.3727017687917805 chr5 180915260 5281219 0.02919167238849835 0.2938889541072275 chr6 171115067 17780972 0.10391236909605395 0.8057888196956756 chr7 159138663 13019966 0.08181522801910181 1.26281526116594 chr8 146364022 17441611 0.11916597235897221 0.8327561504068848 chr9 141213431 10543077 0.0746605823917698 0.7144468322830196 chr10 135534747 13066455 0.09640668012609342 0.6154791976822958 chr11 135006516 5242095 0.038828459213035314 0.43666297682252986 chr12 133851895 3578690 0.02673619226683343 0.3050569920021251 chr13 115169878 9610704 0.08344806964195968 0.5802453377225681 chr14 107349540 4720095 0.043969401266181485 0.42867637463391534 chr15 102531392 4131076 0.04029084087729932 0.4411467418102285 chr16 90354753 8193394 0.09068027666458232 0.5720103935145172 chr17 81195210 6403429 0.078864615289498 0.48104010852457363 chr18 78077248 6999184 0.08964434812046654 1.5483737776443287 chr19 59128983 1476222 0.02496613209126225 0.5998600405924451 chr20 63025520 6954319 0.11034131888162128 0.5706782866638134 chr21 48129895 2734068 0.0568060246131848 0.43224199033408506 chr22 51304566 1089545 0.02123680375738877 0.2328714524988365 chrMT 16571 26875 1.6218091847202944 2.3808928555960827 chrX 155270560 17398656 0.11205379822163326 0.6100114037078739 chrY 59373566 659557 0.011108596711203097 0.2830177507205122