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Table 1 Putative functional mutations in the proposed inversion

From: Structure and decay of a proto-Y region in Tilapia, Oreochromis niloticus

Gene name SNP location on LG1 Reference codon SNP codon Effect on the Y Effect on the X Frequency of SNP in males Frequency of SNP in females
Ras-related protein R-Ras2 (LOC100693950) 10506882 CGA TGA Stop Gain - 0.462 0
Signal peptide 10868192 TCA TGA - Stop Gain 0.545 1
AMP deaminase 3 (LOC100694225) 11096201 TGA TCA Stop Lost - 0.454 0
Zinc finger protein 821 (LOC100712266) 12466312 ATG ACG Start Lost - 0.4 0
Zinc finger protein 821 (LOC100712266) 12466313 ATG ATA Start Lost - 0.4 0
SAFB-like transcription modulator (LOC100711186) 12619332 CGA TGA - Stop Gain 0.613 1
Hepatic lipase (Lipc) 12690753 TGA CGA Stop Lost - 0.448 0
Ammonium transporter Rh type C 2 (LOC100706367) 13529856 ATG ATA - Start Lost 0.575 1
AFG3-like protein 1 (LOC100702885) 13725056 TTA TGA Stop Gain - 0.439 0
CUB and sushi domain-containing protein 1 (LOC100698036) 15189214 CAA TAA Stop Gain - 0.391 0.027
CUB and sushi domain-containing protein 1 (LOC100698036) 15243948 TGC TGA Stop Gain - 0.391 0
Neuromedin-K receptor (LOC100693904) 15788009 CAGG CAGC Splice Site Acceptor Lost - 0.343 0
Protein FAM176A (LOC100700039) 16417062 CGA TGA Stop Gain - 0.475 0
GC-rich sequence DNA-binding factor (LOC100700589) 16480688 CAGA CAGG Splice Site Acceptor Gain - 0.512 0.018
BTB/POZ domain-containing protein KCTD3 (LOC100703295) 16809270 CGA TGA Stop Gain - 0.52 0
Hypothetical protein (LOC100705710) 17489648 CAA TAA - Stop Gain 0.452 0.97
Hypothetical protein (LOC100705710) 17507222 TAA CAA Stop Lost - 0.469 0.04
Nuclear factor of activated T-cells 18194412 TGG TGA - Stop Gain 0.5 0.982
  1. Genes containing a stop codon, start codon or splice site alterations that were in intermediate frequency in males and fixed or nearly fixed in females within the proposed inversion on LG1. Bold denotes the altered SNP.
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