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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