BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084883.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 = 2,636,436 number of mapped reads = 2,350,078 (89.14%) number of supplementary alignments = 16,995 (0.64%) number of secondary alignments = 0 number of mapped bases = 162,975,383 bp number of sequenced bases = 162,913,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,076 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6072 >>>>>>> ACTG content number of A's = 47,458,263 bp (29.13%) number of C's = 29,907,630 bp (18.36%) number of T's = 52,172,702 bp (32.02%) number of G's = 33,348,535 bp (20.47%) number of N's = 25,887 bp (0.02%) GC percentage = 38.83% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,348,213 number of insertions = 13,280 mapped reads with insertion percentage = 0.56% number of deletions = 35,118 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.0526X std coverageData = 0.4759X There is a 4.38% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.11% 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% 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 13362580 0.053611019889896284 1.0397623744620335 chr2 243199373 13713776 0.05638902695690749 0.4216835920557479 chr3 198022430 12040748 0.06080497042683498 0.2848488732307225 chr4 191154276 11640347 0.06089503851852103 0.30278332473957364 chr5 180915260 8881733 0.04909333242535759 0.2759341022953296 chr6 171115067 9495270 0.05549055478557011 0.2759766341233123 chr7 159138663 8943279 0.05619802775394688 0.445848763857403 chr8 146364022 10173694 0.06950952741651223 0.8617804069907395 chr9 141213431 9688563 0.06860935911967184 0.41726436168667685 chr10 135534747 6396755 0.04719642115095401 0.35420821902332456 chr11 135006516 6282356 0.046533724342608766 0.3429749577062724 chr12 133851895 6518993 0.04870303106280266 0.257507014726132 chr13 115169878 6239486 0.054176370665253284 0.26675707838789564 chr14 107349540 3063874 0.028541100409000354 0.2082247764143166 chr15 102531392 4117339 0.04015686239781081 0.22939652431429639 chr16 90354753 3468917 0.038392191720119026 0.2497120283471976 chr17 81195210 3908013 0.04813107817567071 0.2687308810284775 chr18 78077248 4670978 0.05982508502348853 0.7415457540213514 chr19 59128983 3591448 0.06073921481111894 0.5881269510539644 chr20 63025520 2742900 0.04352046599536188 0.2572032961884529 chr21 48129895 1938388 0.0402740957569095 0.2555204637490316 chr22 51304566 1570242 0.030606281709896932 0.19817393557807442 chrMT 16571 119063 7.185022026431718 4.2439752567951965 chrX 155270560 10013296 0.06448934041327603 0.3183515002684118 chrY 59373566 393345 0.006624917896964451 0.1596487292968621