人基因组每条染色体的GC含量GC content of human chromosomes

The GC content is the molar ratio of guanine+cytosine bases in DNA. The human genome is a mosaic of GC-rich and GC-poor regions, of around 300kb in length, called isochores. GC content is an important factor in many experiments and bioinformatic analysis. This is especially true for next-generation sequencing where the DNA being sequenced has gone through multiple rounds of PCR amplification.

  • 1 0.417439
  • 2 0.402438
  • 3 0.396943
  • 4 0.382479
  • 5 0.395163
  • 6 0.396109
  • 7 0.407513
  • 8 0.401757
  • 9 0.413168
  • 10 0.415849
  • 11 0.415657
  • 12 0.40812
  • 13 0.385265
  • 14 0.408872
  • 15 0.42201
  • 16 0.447894
  • 17 0.455405
  • 18 0.39785
  • 19 0.483603
  • 20 0.441257
  • 21 0.408325
  • 22 0.479881
  • X 0.394963
  • Y 0.391288
  • MT 0.443626

The common way to reduce the GC bias in data analysis is to basically

  1. calculate to GC ratio (number of G/C bases / number of bases) in the region of interest (ROI) being measured
  2. find average value measured (a) across the genome in all regions with this ratio
  3. normalize the value measured in the ROI (m) with this value: m/a

More details on the GC bias in next-gen sequencing is described by Benjamini and Speed here: ” The bias is not consistent between samples; and there is no consensus as to the best methods to remove it in a single sample. (…) It is the GC content of the full DNA fragment, not only the sequenced read, that most influences fragment count. This GC effect is unimodal: both GC-rich fragments and AT-rich fragments are underrepresented in the sequencing results. This empirical evidence strengthens the hypothesis that PCR is the most important cause of the GC bias.”

Ref: http://blog.kokocinski.net/index.php/gc-content-of-human-chromosomes?blog=2

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