Table 1 Sequences, alignments and SNPs: summary of data generated and analyzed in this work

Sequences

CL-Brener Reference (CDS); TcVI

Mapped CDS from Sylvio X10 genome; TcI

Mapped transcripts from TcI transcriptome

Mapped reads from Esmeraldo cl3 shotgun; TcII §

Mapped Expressed Sequence Tags (ESTs)

Mapped misc GenBank sequences (mRNAs, CDS)

Alignments

Total

Containing two reference coding sequences

SNPs

Total

With P > 0.70 †

In good sequence neighborhood *

P > 0.70 AND good seq neighborhood †*

  Synonymous †*

  Non-synonymous †*

  Nonsense †*

  Non-coding †*

  Triallelic †*

  Tetra-allelic †*

  Average SNP density †*

Indels

Total

With P > 0.70 †

In good sequence neighborhood *

P > 0.70 AND good seq neighborhood †*