BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085014.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 = 2,234,303 number of mapped reads = 1,989,544 (89.05%) number of supplementary alignments = 9,018 (0.4%) number of secondary alignments = 0 number of mapped bases = 131,908,021 bp number of sequenced bases = 131,850,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,220 duplication rate = 2.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3165 >>>>>>> ACTG content number of A's = 35,920,782 bp (27.24%) number of C's = 26,421,502 bp (20.04%) number of T's = 39,331,026 bp (29.83%) number of G's = 30,170,654 bp (22.88%) number of N's = 6,544 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,291,057 number of insertions = 9,142 mapped reads with insertion percentage = 0.46% number of deletions = 31,817 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.2952X There is a 3.71% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11669063 0.04681658546399369 0.34449710520591736 chr2 243199373 12652810 0.05202649103869195 0.3886951636263 chr3 198022430 8052291 0.04066352988396314 0.22444081529537363 chr4 191154276 6805758 0.03560348291659455 0.2164379070812184 chr5 180915260 6418070 0.035475559109828546 0.2093759353302487 chr6 171115067 9215188 0.053853749769446076 0.33662485586476254 chr7 159138663 11614515 0.07298361555293449 0.4114664462386007 chr8 146364022 7288966 0.04980025760702313 0.3692007550440789 chr9 141213431 4327876 0.03064776465915625 0.2575012903148312 chr10 135534747 9628852 0.0710434203267447 0.3468813901445393 chr11 135006516 5499212 0.04073293766057929 0.3675703025000741 chr12 133851895 5576256 0.04165989581245749 0.231882309389142 chr13 115169878 2618259 0.02273388706724166 0.16534887621349845 chr14 107349540 4523254 0.0421357557750131 0.2351190436865803 chr15 102531392 2297120 0.02240406528373281 0.1740980893133456 chr16 90354753 3975301 0.04399658975328061 0.23955983844144993 chr17 81195210 2348607 0.02892543784294665 0.2275855138547418 chr18 78077248 3198221 0.04096226598560441 0.44770763728731305 chr19 59128983 2468696 0.041751030962260925 0.29973049388790446 chr20 63025520 3447173 0.05469487598039651 0.26259724201288154 chr21 48129895 1479698 0.030743844340404232 0.20709689131546052 chr22 51304566 1093324 0.021310461918730587 0.16064476277225084 chrMT 16571 13510 0.8152797055096253 1.1120358922859663 chrX 155270560 5440026 0.03503578527700293 0.22407497597006076 chrY 59373566 255975 0.004311262018521845 0.09805833279559577