BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819105.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,021,607 number of mapped reads = 2,803,932 (92.8%) number of supplementary alignments = 12,079 (0.4%) number of secondary alignments = 0 number of mapped bases = 165,939,818 bp number of sequenced bases = 165,889,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 205,033 duplication rate = 5.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8051 >>>>>>> ACTG content number of A's = 42,591,910 bp (25.67%) number of C's = 32,995,716 bp (19.89%) number of T's = 51,332,667 bp (30.94%) number of G's = 38,966,634 bp (23.49%) number of N's = 2,531 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 825,818 number of insertions = 10,734 mapped reads with insertion percentage = 0.38% number of deletions = 30,055 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.48% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.4771X There is a 4.35% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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 16551980 0.06640697597299065 0.9574737250212279 chr2 243199373 12980368 0.0533733612874076 0.54649586261561 chr3 198022430 8895171 0.04492001739398915 0.252137575051708 chr4 191154276 9105611 0.047634880006555545 0.34152970648400705 chr5 180915260 8920260 0.04930628848003203 0.2678511661270294 chr6 171115067 7057761 0.04124570164239248 0.32604040929527844 chr7 159138663 8318135 0.05226973032945489 0.6002127758914154 chr8 146364022 15338045 0.10479382016435705 0.5406985773181231 chr9 141213431 7113564 0.05037455679410551 0.3921793297358371 chr10 135534747 8757970 0.06461789462741979 0.4723843163934413 chr11 135006516 5701236 0.04222933950832418 0.43536674739745085 chr12 133851895 7536294 0.05630322977496882 0.28664035422669415 chr13 115169878 3546483 0.03079349445868129 0.21191943230522617 chr14 107349540 3907554 0.03640028639153926 0.23787035266378215 chr15 102531392 4402800 0.04294099508568069 0.2509339912902514 chr16 90354753 5265933 0.058280641860644564 0.32225126156089906 chr17 81195210 5948018 0.07325577457093836 0.3571933537424093 chr18 78077248 3971007 0.050859976519664216 0.7868797849270659 chr19 59128983 3462405 0.05855681637548205 0.6232401840172043 chr20 63025520 4964566 0.07877072652474744 0.3442888657495459 chr21 48129895 2323648 0.04827868417331889 0.31966049569615634 chr22 51304566 1418363 0.027645940909041117 0.19720763383795153 chrMT 16571 11564 0.6978456339388087 0.8913083407150408 chrX 155270560 9868299 0.0635555059503875 0.3491774724912279 chrY 59373566 572783 0.009647104571755046 0.3124710239044695