Variations Between the PGF and COX MHC Haplotypes
|
Context |
SNPs |
Indels |
Total |
bp |
kb-1 |
|---|---|---|---|---|---|
| Codinga,b | 341 | 8 | 349 | 247,604 | 1.41 |
| Exonic UTR | 308 | 26 | 334 | 128,976 | 2.59 |
| Intronic | 2552 | 472 | 3024 | 1,052,077 | 2.87 |
| Pseudogenic | 460 | 33 | 493 | 107,079 | 4.60 |
| Microsatellitec | 262 | 230 | 492 | 28,788 | 17.09 |
| Interspersed repeatsd | 3616 | 719 | 4335 | 1,092,788 | 3.97 |
| Other intergenic | 8474 | 913 | 9387 | 2,097,517 | 4.48 |
| Total | 16,013 | 2401 | 18,414 | 4,754,829 | 3.87 |
| kb-1 | 3.37 | 0.51 | |||
| Transversions | 5189 | ||||
| Transitions
|
10,824
|
|
|
|
|
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Variations are classified according to type and position.
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↵a Coding variations were in 320 codons as follows: 297 with one SNP; 21 with two SNPs; two with three SNPs. Codon changes due to these variations are shown in Table 2.
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↵b Indels within coding regions did not disrupt the reading frame at the end of the exon containing them: either by being multiples of 3 nt, or by pairing with another indel that had an opposite effect on the reading frame.
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↵c Microsatellites were annotated by the Tandem Repeats Finder (Benson 1999) as ≥7 copies of a ≥2-mer.
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↵d Interspersed repeats were annotated by RepeatMasker as LINEs or SINEs.
