BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084810.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,215,821 number of mapped reads = 1,974,728 (89.12%) number of supplementary alignments = 21,418 (0.97%) number of secondary alignments = 0 number of mapped bases = 131,505,420 bp number of sequenced bases = 131,455,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,446 duplication rate = 4.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5149 >>>>>>> ACTG content number of A's = 35,534,095 bp (27.03%) number of C's = 24,655,269 bp (18.76%) number of T's = 41,249,607 bp (31.38%) number of G's = 29,998,458 bp (22.82%) number of N's = 18,466 bp (0.01%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,022,517 number of insertions = 10,204 mapped reads with insertion percentage = 0.51% number of deletions = 29,985 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.3021X There is a 3.39% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 10941971 0.04389947337382963 0.3742186708164696 chr2 243199373 10612065 0.04363524818791371 0.4687333429436989 chr3 198022430 11789519 0.05953628081424917 0.2975287433340355 chr4 191154276 8134425 0.04255424032471029 0.252269854566628 chr5 180915260 7428791 0.04106226860022753 0.24822788084281658 chr6 171115067 6636767 0.03878540397614431 0.2595347668377107 chr7 159138663 7985699 0.05018075965612455 0.3321411337475052 chr8 146364022 6430698 0.04393633020005422 0.2882276229306051 chr9 141213431 9797964 0.06938408004547386 0.37382938369036234 chr10 135534747 3954217 0.029174931798116685 0.2157082690276633 chr11 135006516 5603292 0.04150386341352591 0.2838274485969286 chr12 133851895 5772722 0.043127682278984544 0.2523634877730507 chr13 115169878 3816571 0.03313862154130267 0.22099300141822398 chr14 107349540 2353085 0.021919842413856642 0.18661865673389258 chr15 102531392 3583597 0.034951217671949676 0.23443163525680094 chr16 90354753 2078629 0.023005198188079824 0.18940331331614507 chr17 81195210 3371048 0.04151781860038296 0.25131539757122434 chr18 78077248 4342201 0.05561416560173842 0.4386085430425722 chr19 59128983 2817280 0.04764634629349197 0.31800116840343834 chr20 63025520 2973286 0.04717590588701212 0.26776531044925234 chr21 48129895 954127 0.019823999200496906 0.17733159303725615 chr22 51304566 1109719 0.02163002411910082 0.1751683157218265 chrMT 16571 22629 1.365578420131555 1.436835937183157 chrX 155270560 8731226 0.05623233406255507 0.2959012786404301 chrY 59373566 263892 0.004444604186314159 0.09431964977192225