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Table 3 List of homozygous SNPs located within the coding region. Position of the SNP and CDS coordinates refer to the virulent strain

From: Complete genomes of the eukaryotic poultry parasite Histomonas meleagridis: linking sequence analysis with virulence / attenuation

contig (virulent strain) SNP position CDS start CDS end CDS strand gene ID virulent strain gene ID attenuated strain functional annotation SNP type PROVEAN prediction (threshold ≤ −2.5)
contig_1 808,350 807,890 809,134 g222 g1540 Clan MG, family M24, aminopeptidase P-like metallopeptidase non synonymous missense T262R neutral (score − 0.566)
contig_4 907,239 906,962 907,699 + g6022 g2624 unknown; domain superfamily: PRK05901-RNA polymerase sigma factor, provisional non synonymous missense D93V deleterious
contig_9 56,933 56,370 59,399 + g9263 g1249 Rho-GEF non synonymous missense M188I neutral (score 1.600)
contig_9 754,604 754,419 755,309 g9462 g9315 Ser/Thr protein phosphatase non synonymous missense F236V neutral (score 0.252)
contig_24 8498 8153 9325 + g3899 g1904 guanidine-nucleotide exchange factor domain containing protein non synonymous missense P116S neutral (score 0.717)
contig_24 135,940 135,268 135,959 + g3944 g1860 CAMK family serine/threonine-protein kinase 25-like non synonymous missense M258K deleterious (score − 2906.0)
contig_30 608,903 608,341 611,167 + g4054 g10480 alpha amylase domain-containing protein non synonymous missense S188F neutral (score − 0.233)
contig_39 136,516 136,175 136,771 + g5742 g4148 transposable element Tcb2 transposase synonymous n.d.*
contig_46 126,968 124,401 127,370 g6691 g4310 BspA family leucine-rich repeat surface protein non synonymous missense E135K neutral (score 0.067)
contig_51 970,026 967,493 970,771 + g7214 g10757 Major Facilitator Superfamily transporter non synonymous missense K845M neutral (score − 1.744)
contig_55 233,376 232,271 233,587 + g7655 g5929 Myb-like DNA-binding domain containing protein non synonymous missense R369M neutral (score − 0.712)
contig_68 549,886 546,983 550,105 + g8542 g6202 unknown synonymous n.d.
contig_68 639,193 639,152 640,081 g8565 g6179 hypothetical protein non synonymous missense M297L neutral (score − 1.0)
contig_72 57,296 56,499 58,331 + g8794 g337 leucine rich repeat containing protein non synonymous nonsense W266del deleterious (score − 56.252)
contig_82 121,399 120,392 121,525 + g9013 g1396 type IIB DNA topoisomerase family protein synonymous n.d.
contig_118 307,118 306,262 307,380 g931 g3679 POC1 centriolar protein homolog B non synonymous missense P88R neutral (score 0.655)
scaffold_61 3,064,020 3,064,015 3,066,186 + G10965 G6535 chitinase-like protein synonymous n.d.
  1. *n.d. not done