BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082145.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 = 1,801,294 number of mapped reads = 1,640,124 (91.05%) number of supplementary alignments = 14,012 (0.78%) number of secondary alignments = 0 number of mapped bases = 112,271,092 bp number of sequenced bases = 112,231,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,670 duplication rate = 2.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0461 >>>>>>> ACTG content number of A's = 32,523,216 bp (28.98%) number of C's = 21,134,572 bp (18.83%) number of T's = 34,176,705 bp (30.45%) number of G's = 24,394,101 bp (21.74%) number of N's = 2,452 bp (0%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 938,279 number of insertions = 9,124 mapped reads with insertion percentage = 0.55% number of deletions = 24,403 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.27% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.328X There is a 3.26% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8849678 0.03550513922290288 0.5479425714821674 chr2 243199373 9650946 0.03968326842684747 0.36933772816128335 chr3 198022430 7717325 0.03897197403344661 0.21369910650944 chr4 191154276 7602242 0.039770190649567265 0.22096816846883532 chr5 180915260 7021448 0.03881070065620777 0.21376819324732468 chr6 171115067 6730126 0.03933099590815109 0.24207905051100945 chr7 159138663 6251308 0.039282144779612733 0.42014786794124614 chr8 146364022 5879514 0.04017048670608409 0.6022509559069228 chr9 141213431 4704846 0.03331726994155393 0.3000213002631445 chr10 135534747 5197176 0.03834570923720395 0.2977264567749363 chr11 135006516 5025175 0.037221721950072395 0.26434627831465596 chr12 133851895 4999457 0.037350662835217985 0.21093870905844012 chr13 115169878 3724571 0.03233980155818173 0.19294297546975314 chr14 107349540 3440359 0.03204819508309025 0.20620121229900007 chr15 102531392 3108732 0.030319806835354388 0.19181714019008297 chr16 90354753 2983194 0.0330164590234672 0.2182660919631953 chr17 81195210 2716381 0.03345494149223827 0.213686418079209 chr18 78077248 3074301 0.039375119881274505 0.5104189424241192 chr19 59128983 1963310 0.03320385199251609 0.42112693586089067 chr20 63025520 2162380 0.03430959395495666 0.20344939914757768 chr21 48129895 1485506 0.030864517780477187 0.2003224756419285 chr22 51304566 1106997 0.021576968412519073 0.15784346758125667 chrMT 16571 1289 0.07778649447830548 0.288237535289196 chrX 155270560 6600052 0.04250678299865731 0.24004646101055044 chrY 59373566 274779 0.00462796861485463 0.10516523603325632