Table 1

Sequences, alignments and SNPs: summary of data generated and analyzed in this work
Description Number
Sequences
CL-Brener Reference (CDS); TcVI 25,013
Mapped CDS from Sylvio X10 genome; TcI 4,918
Mapped transcripts from TcI transcriptome 3,486
Mapped reads from Esmeraldo cl3 shotgun; TcII § 134,424
Mapped Expressed Sequence Tags (ESTs) 13,968
Mapped misc GenBank sequences (mRNAs, CDS) 2,038
Alignments
Total 7,639
Containing two reference coding sequences 5,447
SNPs
Total 325,355
With P > 0.70 † 305,993
In good sequence neighborhood * 302,390
P > 0.70 AND good seq neighborhood †* 288,957
  Synonymous †* 125,455
  Non-synonymous †* 162,820
  Nonsense †* 113
  Non-coding †* 569
  Triallelic †* 2,990
  Tetra-allelic †* 10
  Average SNP density †* 2.4 per 100 bp
Indels
Total 28,316
With P > 0.70 † 11,007
In good sequence neighborhood * 10,523
P > 0.70 AND good seq neighborhood †* 1,480

§ reads where at least 50bp matched the reference with >= 95% identity.

† SNPs with probability > 0.7 as assigned by PolyBayes [34].

* SNP is located in a 10 bp window with < 2 other SNPs.

Ackermann et al.

Ackermann et al. BMC Genomics 2012 13:736   doi:10.1186/1471-2164-13-736

Open Data