BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708649.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 = 5,074,405 number of mapped reads = 4,881,861 (96.21%) number of supplementary alignments = 184 (0%) number of secondary alignments = 0 number of mapped bases = 243,415,077 bp number of sequenced bases = 243,392,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,717 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.383 >>>>>>> ACTG content number of A's = 75,306,011 bp (30.94%) number of C's = 46,202,196 bp (18.98%) number of T's = 75,232,683 bp (30.91%) number of G's = 46,643,308 bp (19.16%) number of N's = 7,844 bp (0%) GC percentage = 38.15% >>>>>>> Mismatches and indels general error rate = 0.0018 number of mismatches = 407,361 number of insertions = 18,249 mapped reads with insertion percentage = 0.37% number of deletions = 13,607 mapped reads with deletion percentage = 0.28% homopolymer indels = 48.86% >>>>>>> Coverage mean coverageData = 0.0786X std coverageData = 0.6198X There is a 3.71% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 39402173 0.15808254696384488 0.8982588111694509 chr2 243199373 9843202 0.04047379678071785 0.3343892617728409 chr3 198022430 17161415 0.08666399558878254 0.6483914190559036 chr4 191154276 15854455 0.08294062435725999 0.6253495192887413 chr5 180915260 22806259 0.12606044951653056 0.7846428577532388 chr6 171115067 5277468 0.030841632432052287 0.3032862729572737 chr7 159138663 6677132 0.04195794959016339 0.3897066153984836 chr8 146364022 14877506 0.10164728870323063 0.6658934324249782 chr9 141213431 22527262 0.15952634137187702 1.0745618470639617 chr10 135534747 11300847 0.08337970336123474 0.5515572804623861 chr11 135006516 14585277 0.10803387445388192 0.7648359292998055 chr12 133851895 11983497 0.08952803395125634 0.6087018056740413 chr13 115169878 2104876 0.018276271856431072 0.18054415487359413 chr14 107349540 2888808 0.026910296960750833 0.3388239831415802 chr15 102531392 1828454 0.017833113979375214 0.1864428823440217 chr16 90354753 2736143 0.030282225440868615 0.2668090829987101 chr17 81195210 4795701 0.0590638413275857 0.4570276876287005 chr18 78077248 20192860 0.25862668725209165 1.2995359374481337 chr19 59128983 1210454 0.020471415853710862 0.32447274678813703 chr20 63025520 10781345 0.17106316615872427 0.9089902692462416 chr21 48129895 1188712 0.024697996951790566 0.20351643415240578 chr22 51304566 548498 0.01069101724786055 0.1254701116939027 chrMT 16571 50 0.003017319413433106 0.05484719862481972 chrX 155270560 2528509 0.016284535845043645 0.2187890950611037 chrY 59373566 314174 0.005291479376529279 0.08122302001193277