BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080998.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 = 3,213,869 number of mapped reads = 2,836,886 (88.27%) number of supplementary alignments = 16,397 (0.51%) number of secondary alignments = 0 number of mapped bases = 182,606,928 bp number of sequenced bases = 182,546,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,073 duplication rate = 3.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0046 >>>>>>> ACTG content number of A's = 50,990,213 bp (27.93%) number of C's = 36,545,839 bp (20.02%) number of T's = 54,109,960 bp (29.64%) number of G's = 40,897,750 bp (22.4%) number of N's = 2,294 bp (0%) GC percentage = 42.42% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,303,756 number of insertions = 12,310 mapped reads with insertion percentage = 0.43% number of deletions = 34,668 mapped reads with deletion percentage = 1.21% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.059X std coverageData = 0.3758X There is a 4.68% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14553988 0.05839097989649542 0.5482663605511491 chr2 243199373 15836969 0.06511928383960101 0.42321732531314354 chr3 198022430 11999221 0.06059526185998222 0.30030373879334116 chr4 191154276 11809049 0.06177758220799623 0.31718883556340033 chr5 180915260 11493747 0.06353110843164916 0.3078245694770929 chr6 171115067 10936909 0.06391552299716541 0.3989626761587864 chr7 159138663 9805411 0.061615517028693396 0.47509443859327105 chr8 146364022 8914217 0.06090442772883079 0.3889460665472427 chr9 141213431 7949129 0.056291593113405765 0.3539031052771691 chr10 135534747 8618774 0.06359088123726678 0.36143188909272295 chr11 135006516 8361711 0.0619356105745296 0.36235582575272746 chr12 133851895 8444680 0.06308973063100826 0.3078156862201229 chr13 115169878 5802212 0.05037959665113129 0.27354247965165046 chr14 107349540 5478573 0.05103489963720385 0.2855578015916734 chr15 102531392 5107141 0.04981051071656181 0.28467513066156896 chr16 90354753 5383091 0.059577286432292056 0.32290341595635236 chr17 81195210 4772085 0.058772986731606455 0.31459139727833485 chr18 78077248 4720138 0.060454717871203656 0.5823805012994384 chr19 59128983 3737127 0.06320296427219119 0.43522158243090153 chr20 63025520 3836609 0.06087389679609149 0.31032292315761906 chr21 48129895 2365979 0.04915819990880928 0.29040522846362027 chr22 51304566 2069418 0.040335942029019405 0.24337738836115635 chrMT 16571 48785 2.9439985516866813 2.338286864105626 chrX 155270560 10119813 0.06517534940300337 0.3353147430724126 chrY 59373566 442152 0.0074469503819258554 0.15558581885990302