BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR975274.sorted.bam
outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,509,750
number of mapped reads = 2,480,339 (98.83%)
number of supplementary alignments = 27,491 (1.1%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 1,242,005
number of mapped paired reads (second in pair) = 1,238,334
number of mapped paired reads (both in pair) = 2,472,608
number of mapped paired reads (singletons) = 7,731
number of mapped bases = 334,660,538 bp
number of sequenced bases = 334,417,147 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 377,894
duplication rate = 14.97%
>>>>>>> Insert size
mean insert size = 78,332.8173
std insert size = 2,693,377.0766
median insert size = 169
>>>>>>> Mapping quality
mean mapping quality = 53.7345
>>>>>>> ACTG content
number of A's = 97,657,503 bp (29.2%)
number of C's = 67,834,277 bp (20.28%)
number of T's = 97,337,600 bp (29.11%)
number of G's = 71,566,872 bp (21.4%)
number of N's = 20,895 bp (0.01%)
GC percentage = 41.68%
>>>>>>> Mismatches and indels
general error rate = 0.0107
number of mismatches = 3,434,984
number of insertions = 66,234
mapped reads with insertion percentage = 2.55%
number of deletions = 128,485
mapped reads with deletion percentage = 4.99%
homopolymer indels = 46.64%
>>>>>>> Coverage
mean coverageData = 0.1081X
std coverageData = 1.1989X
There is a 5.99% of reference with a coverageData >= 1X
There is a 3.39% of reference with a coverageData >= 2X
There is a 0.56% of reference with a coverageData >= 3X
There is a 0.26% of reference with a coverageData >= 4X
There is a 0.07% of reference with a coverageData >= 5X
There is a 0.04% of reference with a coverageData >= 6X
There is a 0.02% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% 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 31848231 0.12777593440780233 1.3818033414486257
chr2 243199373 28673476 0.11790110988485156 1.1873581121291483
chr3 198022430 23905948 0.12072343521892949 0.5100551237841894
chr4 191154276 11985560 0.06270097771707707 0.7752967872188673
chr5 180915260 21117669 0.11672685322399005 0.4838107266763543
chr6 171115067 27763451 0.1622501833809877 1.0183537497341197
chr7 159138663 19928725 0.12522868185715497 1.3099161623600766
chr8 146364022 17465895 0.11933188744977233 0.5880883869102054
chr9 141213431 14675500 0.10392425066139778 1.7146477460441727
chr10 135534747 18772331 0.13850567043150935 3.1801308246244893
chr11 135006516 12530099 0.09281106846724346 1.2530964074454978
chr12 133851895 14946380 0.11166356666074843 0.47014459736125225
chr13 115169878 11499704 0.09984992777364929 0.44778163814173394
chr14 107349540 10146424 0.09451762904619805 0.44480275312744083
chr15 102531392 9885399 0.0964133891793842 0.4374480689047919
chr16 90354753 11418841 0.12637786747090107 1.6369785262953724
chr17 81195210 7206265 0.08875234142506683 1.008178318795499
chr18 78077248 9567914 0.12254420135299851 1.5829699842647966
chr19 59128983 4592424 0.07766790103594375 0.8467137594273584
chr20 63025520 3710066 0.058866091069141514 0.4073810655861773
chr21 48129895 4314896 0.08965105783006591 0.6248078599812784
chr22 51304566 3575206 0.06968592230173042 0.3782113434874109
chrMT 16571 73270 4.421579868444874 3.553281888281512
chrX 155270560 10502281 0.06763858518961997 0.5196076713330178
chrY 59373566 4554583 0.07671061899836032 1.768389270708434