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Table 2 Number of methylated 1 kb windows called by three methods.

From: Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

    No. methylated 1 kb windows   
All Tissues RPKM CPPD NB Common Agreement NB
Methylated 13,715 14,036 2,335 1,096 46.9
Unmethylated 252,104 252,421 301,637 233,368 77.4
Tissue-specific 112,717 112,079 74,564 60,003 80.5
Tissue-specific proportion 0.89 0.89 0.97   
    No. methylated 1 kb windows   
By Tissue RPKM CPPD NB Common Agreement NB
Bud 74,265 88,975 54,805 44,101 80.5
Male catkin 60,010 63,136 17,521 14,154 80.8
Female catkin 73,830 74,568 32,922 29,388 89.3
Leaf 66,951 63,207 26,858 20,937 97.5
Root 65,843 42,548 21,469 24,080 89.7
Phloem 61,792 71,652 6,499 4,838 74.4
Xylem 48,392 34,174 14,659 9,185 62.7
  1. Number of 1 kb windows in each of seven tissues (bud, male catkin, female catkin, leaf, root, phloem, xylem) called methylated using RPKM cutoff (1% FDR), cumulative Poisson probability distribution (CPPD), or a negative binomial analysis (NB). "Common" refers to the number of 1 kb windows called methylated by all three of the analytic methods. Percent agreement NB refers to the percent of windows called by the NB method that were also in common with those called by both RPKM and CPPD. Tissue specific proportion is proportion of tissue-specific called windows as a fraction of all the windows in the genome that were found to be methylated in any tissues.