BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081936.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 = 2,921,627 number of mapped reads = 2,652,370 (90.78%) number of supplementary alignments = 14,837 (0.51%) number of secondary alignments = 0 number of mapped bases = 182,216,961 bp number of sequenced bases = 182,144,713 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,803 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1066 >>>>>>> ACTG content number of A's = 51,785,806 bp (28.43%) number of C's = 33,986,592 bp (18.66%) number of T's = 57,076,281 bp (31.34%) number of G's = 39,272,364 bp (21.56%) number of N's = 23,670 bp (0.01%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,459,362 number of insertions = 14,083 mapped reads with insertion percentage = 0.53% number of deletions = 40,892 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.0589X std coverageData = 0.6235X There is a 5% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 16522267 0.066287766641111 1.1771418760455359 chr2 243199373 15861214 0.06521897570846122 0.8484779968963053 chr3 198022430 11637273 0.058767448717804344 0.27738468322075843 chr4 191154276 9256439 0.04842391807128604 0.284781533646018 chr5 180915260 9039173 0.049963574106462884 0.2602066890837986 chr6 171115067 15658394 0.09150797924767198 0.4960013933405577 chr7 159138663 12320650 0.07742084649787462 0.9237230824886413 chr8 146364022 10280227 0.07023739071614198 0.8472529638050315 chr9 141213431 8799148 0.062310985135684435 0.6735921690760814 chr10 135534747 7474262 0.055146463659241564 0.6018144893860985 chr11 135006516 8476897 0.06278879902359676 0.44047320758663455 chr12 133851895 7700795 0.057532207519363096 0.28738299297169106 chr13 115169878 4800874 0.04168515312658402 0.22881015342771732 chr14 107349540 4566330 0.04253702437849291 0.29318086186087466 chr15 102531392 4232315 0.041278236035262254 0.23578963689822124 chr16 90354753 3872132 0.04285476824888227 0.3212285589473995 chr17 81195210 5025211 0.06189048590427933 0.32088794780396923 chr18 78077248 5271326 0.06751423923138275 1.0914574379131572 chr19 59128983 3966931 0.06708945087048089 0.8306832534261621 chr20 63025520 4589033 0.07281229889098892 0.31765925420846564 chr21 48129895 1984354 0.04122913627798274 0.2811990210287274 chr22 51304566 1451750 0.02829670170097531 0.18558221171053071 chrMT 16571 19428 1.1724096312835677 1.2831366060556424 chrX 155270560 8979889 0.0578338160176662 0.35049834194068236 chrY 59373566 430649 0.007253210965970951 0.20110503294378865