Table 2 The different categories (Cat) of synonymous and non-synonymous codon substitutions among the N. tetrasperma mat a and mat A chromosomes

Cat	mat Allele-specific substitution	Type of change	NC	NTa	NTA	Pseudoautosomal region 1		Stratum 2		Stratum 1		Pseudoautosomal region 2
						No. codons	No. per 1000 codons	No. codons	No. per 1000 codons	No. codons	No. per 1000 codons	No. codons	No. per 1000 codons
1	No	None	Codon1 (AA1)	Codon1 (AA1)	Codon1 (AA1)	5238	932.36	10 990	944.80	51 513	945.08	10 422	944.19
2	No	Shared Synonymous	Codon1 (AA1)	Codon2 (AA1)	Codon2 (AA1)	333	59.27	522	44.88	1712	31.41	515	46.66
3	No	Shared Non-synonymous	Codon1 (AA1)	Codon2 (AA2)	Codon2 (AA2)	45	8.01	81	6.96	363	6.66	101	9.15
4	Yes, *mat a*	Non-synonymous	Codon1 (AA1)	Codon2 (AA2)	Codon1 (AA1)	0	0	6	0.52	116	2.13	0	0
5	Yes, *mat A*	Non-synonymous	Codon1 (AA1)	Codon1 (AA1)	Codon2 (AA2)	0	0	13	1.12	117	2.15	0	0
6	Yes, *mat a*	Synonymous	Codon1 (AA1)	Codon2 (AA1)	Codon1 (AA1)	0	0	11	0.95	320	5.87	0	0
7	Yes, *mat A*	Synonymous	Codon1 (AA1)	Codon1 (AA1)	Codon2 (AA1)	2	0.35	8	0.69	350	6.42	0	0
8	Yes (excluded)^a	Non-synonymous Both	Codon1 (AA1)	Codon2 (AA2)	Codon3 (AA3)	0	0	0	0	5	0.09	0	0
9	Yes (excluded)^a	Synonymous Both	Codon1 (AA1)	Codon 2 (AA1)	Codon3 (AA1)	0	0	0	0	10	0.18	0	0
Total number of codons						5618		11 631		54 506		11 038

Abbreviations: AA, Amino acid; Nta, N. tetrasperma mat a; NTA, N. tetrasperma mat A.
The type of substitution was determined based on comparison of codons and amino acids (AA) to the closely related and normally recombining mat chromosomes from N crassa (NC). Data is based on concatenated sequences for each genomic region. Allele-specific substitutions are in bold. Codons and amino acids followed by different numbers within a single category are indicative of a substitution.
^aCodon positions that have switched to different codons on both the mat a and mat A chromosomes were not included in allele-specific counts and were categorized separately.

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