Description Format Source References

for each position in mate 2 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 0.9992, the probability of making an error by
sequencing a T is 0.0002, the probability of making an error by
sequencing a G is 0.0002, the probability of making an error by
sequencing a C is 0.0001, and the probability of reading an 'N' at
position 8 is 0.0002. This can be seen by looking at
`model5[model5$pos == 8,]`

. Note that position indexing is 1-based,
though a 0 position is included as described in the GemSIM documentation.

data frame named `model5`

, 7 columns, 505 rows

processed from the Illumina v5 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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