BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080950.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 = 2,945,543 number of mapped reads = 2,434,856 (82.66%) number of supplementary alignments = 13,197 (0.45%) number of secondary alignments = 0 number of mapped bases = 163,861,363 bp number of sequenced bases = 163,803,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,037 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6939 >>>>>>> ACTG content number of A's = 45,667,192 bp (27.88%) number of C's = 29,291,321 bp (17.88%) number of T's = 53,030,330 bp (32.37%) number of G's = 35,492,953 bp (21.67%) number of N's = 322,005 bp (0.2%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,590,176 number of insertions = 12,079 mapped reads with insertion percentage = 0.49% number of deletions = 33,226 mapped reads with deletion percentage = 1.35% homopolymer indels = 49.68% >>>>>>> Coverage mean coverageData = 0.0529X std coverageData = 0.3765X There is a 4.34% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% 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 13336788 0.0535075417124036 0.6518663778296027 chr2 243199373 14657918 0.06027119979458171 0.4018285034228856 chr3 198022430 11801693 0.05959775869834544 0.28525442158857534 chr4 191154276 9731034 0.05090670323273334 0.2703641208603375 chr5 180915260 11208302 0.06195332555142115 0.2936440750408892 chr6 171115067 9584452 0.056011736242957494 0.30863627804836624 chr7 159138663 7918005 0.04975538219772526 0.38520441477620343 chr8 146364022 8428066 0.05758290790888487 0.5405661890447452 chr9 141213431 7002536 0.04958831430134999 0.38675282649663323 chr10 135534747 7927720 0.05849215920991833 0.32848806855277146 chr11 135006516 6694986 0.04959009534028713 0.30717075315900594 chr12 133851895 7490877 0.05596392191533785 0.28045048657699984 chr13 115169878 5657048 0.049119162911677304 0.2611060367227549 chr14 107349540 5091260 0.04742693820579017 0.2683646138632849 chr15 102531392 5358233 0.05225943874828111 0.26822993507659915 chr16 90354753 4548310 0.05033835906784007 0.28225578471445134 chr17 81195210 4264289 0.05251897248618484 0.28924647537750614 chr18 78077248 4536666 0.058104839965670924 0.6164012887236747 chr19 59128983 2572265 0.043502608526177426 0.49975641742645144 chr20 63025520 3598241 0.057091809793873974 0.28896670598491403 chr21 48129895 2294541 0.04767392490675494 0.2665229419544777 chr22 51304566 1819606 0.03546674578633021 0.21993210876300523 chrMT 16571 27416 1.6544565807736407 1.714616984367775 chrX 155270560 7988924 0.051451633844819 0.2860802235114925 chrY 59373566 322187 0.005426438425477089 0.1164065267849226