BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080698.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 = 3,033,109 number of mapped reads = 2,555,017 (84.24%) number of supplementary alignments = 28,588 (0.94%) number of secondary alignments = 0 number of mapped bases = 175,237,542 bp number of sequenced bases = 175,171,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,623 duplication rate = 5.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2204 >>>>>>> ACTG content number of A's = 51,921,402 bp (29.64%) number of C's = 32,316,909 bp (18.45%) number of T's = 54,459,133 bp (31.09%) number of G's = 36,471,585 bp (20.82%) number of N's = 2,461 bp (0%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,448,747 number of insertions = 13,468 mapped reads with insertion percentage = 0.52% number of deletions = 37,522 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.0566X std coverageData = 0.4986X There is a 3.63% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13393693 0.05373584605833339 0.5307086042780387 chr2 243199373 16233361 0.06674918935749065 0.4759799033523594 chr3 198022430 11803850 0.059608651403782895 0.34938203679422064 chr4 191154276 11786942 0.0616619321662467 0.3633401315210311 chr5 180915260 10551542 0.058323117685042156 0.3463422985218581 chr6 171115067 10457358 0.06111301700860743 0.36323027115514156 chr7 159138663 10478234 0.06584342109245947 0.9015657532090073 chr8 146364022 9026739 0.061673209554189486 1.135483542304706 chr9 141213431 6835315 0.04840414223771675 0.34977008285349664 chr10 135534747 7611986 0.05616261636582389 0.4198461061068266 chr11 135006516 7825174 0.05796145424566026 0.3783540668868292 chr12 133851895 8258481 0.0616986483456211 0.355378940531725 chr13 115169878 6110151 0.05305337737702561 0.3333256043000336 chr14 107349540 5633624 0.052479256082513255 0.33268957951656186 chr15 102531392 4697051 0.0458108576151975 0.3023649942201102 chr16 90354753 4392118 0.04860970623205622 0.31764163824901304 chr17 81195210 4375142 0.053884237752448695 0.3691809474229485 chr18 78077248 4223862 0.054098499988114335 0.4396886874916197 chr19 59128983 2678222 0.04529457237578397 0.3985312041978911 chr20 63025520 3022480 0.047956446848832025 0.31057447313928177 chr21 48129895 2253011 0.04681105163433247 0.3174419806404672 chr22 51304566 1599341 0.03117346319623871 0.24540324303639316 chrMT 16571 673904 40.66767243980448 23.492752569240047 chrX 155270560 10912562 0.07028094701274987 0.3971519743600212 chrY 59373566 403399 0.006794252512978587 0.14333190284896855