BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472678.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,451,626
number of mapped reads = 13,723,186 (94.96%)
number of supplementary alignments = 94,174 (0.65%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,595,093
number of mapped paired reads (second in pair) = 7,128,093
number of mapped paired reads (both in pair) = 13,049,292
number of mapped paired reads (singletons) = 673,894
number of mapped bases = 1,336,416,617 bp
number of sequenced bases = 1,336,214,638 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 9,221,797
duplication rate = 45.68%
>>>>>>> Insert size
mean insert size = 31,882.7195
std insert size = 1,750,836.1238
median insert size = 226
>>>>>>> Mapping quality
mean mapping quality = 54.3264
>>>>>>> ACTG content
number of A's = 372,138,352 bp (27.85%)
number of C's = 304,620,248 bp (22.8%)
number of T's = 359,561,447 bp (26.91%)
number of G's = 299,636,057 bp (22.42%)
number of N's = 258,534 bp (0.02%)
GC percentage = 45.22%
>>>>>>> Mismatches and indels
general error rate = 0.0098
number of mismatches = 12,906,697
number of insertions = 85,651
mapped reads with insertion percentage = 0.62%
number of deletions = 76,422
mapped reads with deletion percentage = 0.55%
homopolymer indels = 45.92%
>>>>>>> Coverage
mean coverageData = 0.4317X
std coverageData = 24.7505X
There is a 2.91% of reference with a coverageData >= 1X
There is a 1.26% of reference with a coverageData >= 2X
There is a 0.64% of reference with a coverageData >= 3X
There is a 0.5% of reference with a coverageData >= 4X
There is a 0.4% of reference with a coverageData >= 5X
There is a 0.36% of reference with a coverageData >= 6X
There is a 0.33% of reference with a coverageData >= 7X
There is a 0.31% of reference with a coverageData >= 8X
There is a 0.3% of reference with a coverageData >= 9X
There is a 0.28% of reference with a coverageData >= 10X
There is a 0.27% of reference with a coverageData >= 11X
There is a 0.26% of reference with a coverageData >= 12X
There is a 0.25% of reference with a coverageData >= 13X
There is a 0.24% of reference with a coverageData >= 14X
There is a 0.23% of reference with a coverageData >= 15X
There is a 0.23% of reference with a coverageData >= 16X
There is a 0.22% of reference with a coverageData >= 17X
There is a 0.21% of reference with a coverageData >= 18X
There is a 0.21% of reference with a coverageData >= 19X
There is a 0.2% of reference with a coverageData >= 20X
There is a 0.2% of reference with a coverageData >= 21X
There is a 0.19% of reference with a coverageData >= 22X
There is a 0.19% of reference with a coverageData >= 23X
There is a 0.19% of reference with a coverageData >= 24X
There is a 0.18% of reference with a coverageData >= 25X
There is a 0.18% of reference with a coverageData >= 26X
There is a 0.17% of reference with a coverageData >= 27X
There is a 0.17% of reference with a coverageData >= 28X
There is a 0.17% of reference with a coverageData >= 29X
There is a 0.16% of reference with a coverageData >= 30X
There is a 0.16% of reference with a coverageData >= 31X
There is a 0.16% of reference with a coverageData >= 32X
There is a 0.16% of reference with a coverageData >= 33X
There is a 0.15% of reference with a coverageData >= 34X
There is a 0.15% of reference with a coverageData >= 35X
There is a 0.15% of reference with a coverageData >= 36X
There is a 0.15% of reference with a coverageData >= 37X
There is a 0.14% of reference with a coverageData >= 38X
There is a 0.14% of reference with a coverageData >= 39X
There is a 0.14% of reference with a coverageData >= 40X
There is a 0.14% of reference with a coverageData >= 41X
There is a 0.14% of reference with a coverageData >= 42X
There is a 0.13% of reference with a coverageData >= 43X
There is a 0.13% of reference with a coverageData >= 44X
There is a 0.13% of reference with a coverageData >= 45X
There is a 0.13% of reference with a coverageData >= 46X
There is a 0.13% of reference with a coverageData >= 47X
There is a 0.12% of reference with a coverageData >= 48X
There is a 0.12% of reference with a coverageData >= 49X
There is a 0.12% of reference with a coverageData >= 50X
There is a 0.12% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 134141070 0.5381774755939325 22.67440965371252
chr2 243199373 107272392 0.4410882753386046 18.81351904299499
chr3 198022430 111706773 0.5641117170413473 15.456696986847133
chr4 191154276 22543475 0.11793340683626664 5.753024321616748
chr5 180915260 81272353 0.4492288433822553 56.394233771946894
chr6 171115067 115068400 0.6724621157995397 25.69311050391257
chr7 159138663 68767492 0.4321230975781165 21.950822181928178
chr8 146364022 57988151 0.39619129214691845 14.50792294959499
chr9 141213431 100582557 0.7122733035216742 21.25945133696379
chr10 135534747 27807869 0.20517151221745372 9.159857997655662
chr11 135006516 23244744 0.1721749785765896 7.528702526189385
chr12 133851895 39196219 0.29283275369392414 9.798272526706416
chr13 115169878 35144701 0.30515532021315506 12.547265234080774
chr14 107349540 19268616 0.17949416457676484 9.886367567681974
chr15 102531392 9659439 0.09420957632175715 6.856786340566071
chr16 90354753 105244493 1.1647919949490648 47.77135585613253
chr17 81195210 54826776 0.6752464338721459 47.42687397329633
chr18 78077248 6705482 0.08588266328239438 5.267281914556507
chr19 59128983 43122092 0.7292885791727552 33.68752781197121
chr20 63025520 52313918 0.8300434173331692 23.8012933981355
chr21 48129895 9985277 0.2074651731527775 18.920553230569492
chr22 51304566 38338446 0.7472716171110384 44.418477795875624
chrMT 16571 5325 0.3213445175306258 0.8899184280552848
chrX 155270560 71184168 0.45845244584678513 24.221598295895593
chrY 59373566 1026389 0.017286969086546023 0.7536666874757788