BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708567.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,692,952 number of mapped reads = 3,022,452 (81.84%) number of supplementary alignments = 88 (0%) number of secondary alignments = 0 number of mapped bases = 150,711,597 bp number of sequenced bases = 150,698,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,921 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4933 >>>>>>> ACTG content number of A's = 46,650,204 bp (30.96%) number of C's = 28,627,650 bp (19%) number of T's = 46,472,654 bp (30.84%) number of G's = 28,940,364 bp (19.2%) number of N's = 7,452 bp (0%) GC percentage = 38.2% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 243,848 number of insertions = 10,250 mapped reads with insertion percentage = 0.34% number of deletions = 8,003 mapped reads with deletion percentage = 0.26% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.0487X std coverageData = 0.2267X There is a 4.63% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 11980296 0.04806526038705436 0.22596187706082052 chr2 243199373 12432587 0.05112096650018913 0.23174875561408823 chr3 198022430 11008588 0.05559263160238969 0.24146636192185517 chr4 191154276 11074437 0.057934550205928956 0.24636321255305638 chr5 180915260 10562257 0.05838234430860061 0.24749325125376737 chr6 171115067 9735610 0.056895106729555264 0.24446511984723907 chr7 159138663 7851676 0.049338582164662276 0.2276082641579562 chr8 146364022 8215749 0.05613229868744656 0.2425595355950664 chr9 141213431 5903382 0.041804677913391965 0.21043689358087886 chr10 135534747 6186599 0.045645851982148905 0.21850132817770684 chr11 135006516 6812882 0.050463356894566484 0.23094498503936806 chr12 133851895 6802258 0.05081928798990855 0.23141265422589802 chr13 115169878 5918704 0.05139107640628047 0.23302367908787444 chr14 107349540 4634487 0.04317193161703348 0.2134720085127926 chr15 102531392 4273620 0.041681088266118535 0.2105584607407918 chr16 90354753 3102974 0.03434212254445541 0.19076321030528165 chr17 81195210 2616542 0.032225324621982014 0.18450896138835682 chr18 78077248 4284178 0.05487101697027026 0.2393304835407368 chr19 59128983 1325619 0.0224191070561792 0.15273852568245233 chr20 63025520 2398378 0.03805407714208467 0.20034776241614452 chr21 48129895 2025534 0.04208473756279751 0.21236596552666817 chr22 51304566 889927 0.01734596098132864 0.13466882966205693 chrMT 16571 250 0.01508659706716553 0.12189746369838267 chrX 155270560 10437083 0.06721868588610745 0.26648517306179326 chrY 59373566 237980 0.004008181014426521 0.06554538093924912