for each position in mate 1 of a paired-end read generated with
the specified Illumina chemistry, this data frame contains the probability
of not making a sequencing error, and of making each of the 4 possible
types of sequencing errors. The reference base (truth) is in column 1,
and the probabilities of sequencing that base given its read position
(column 7) as each of the 5 possible bases (A, T, G, C, and N) is given
in columns 2 through 6, respectively. So for example, at position 8 in
mate 1 of a read where the true base is A, the probability of correctly
calling that base an A is 0.9998, the probability of making an error by
sequencing a T is 2.64e-05, the probability of making an error by
sequencing a G is 1.58e-04, the probability of making an error by
sequencing a C is 3.05e-05, and the probability of reading an 'N' at
position 8 is 0. This can be seen by looking at
model1[model1$pos == 8,]. Note that position indexing is 1-based,
though a 0 position is included as described in the GemSIM documentation.
data frame named
model1, 7 columns, 505 rows
processed from the Illumina v4 error model that ships with GemSIM (see references)
McElroy KE, Luciani F, Thomas T (2012). GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics 13(1), 74.
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