TABLES:

Coding_polymorphisms_and_effects.csv

Noncoding_polymorphisms.csv

Polymorphisms_in_genes.no_effect_calculated.csv

SNPs_in_common_with_potato.csv

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These tables contain polymorphisms in all 6 species:
SLY-> S. lycopersicum var. M82
SPI-> S. pimpinellifollium LA1589
SGA-> S. galapagense LA0530
SCH-> S. chmielewskii LA1840
SHA-> S. habrochaites LA1777
SPE-> S. pennellii LA0716

==> Noncoding_polymorphisms.csv <==
These are SNPs, insertions and deletions found in intergenic regions indicated by the reference annotaion ITAG version 2.3 (www.solgenomics.net)

chr -> chromosome from the S. lycopersicum reference genome v 2.40 (www.solgenomics.net)
pos -> position based on chromosomes from the S. lycopersicum reference genome v 2.40 (www.solgenomics.net)
ref -> can be 'INS' for insertions or the reference base from the S. lycopersicum reference genome v 2.40 (www.solgenomics.net)

For each species analyzed:
call.SLY -> the nucleotide/s call in UIPAC standards or 'del' for deletions.
freq.SLY -> the frequency of reads containing a similar nucleotide to the nucleotide call. In heterozygous calls the frequency corresponds to the most abundant base
cov.SLY -> Total number of reads overlaping the position, both matching and not matching reads are counted. To calculate the number of reads supporting the nucleotide call multiply this number by the frequency in the previous column.
score.SLY -> quality of the call. It ranges from 0 to 5. A minimum quality of 2 is strongly recommended to consider a SNP.

==> Coding_polymorphisms_and_effects.csv <==
These are homozygous SNPs found in coding regions indicated by the reference annotation ITAG v2.3 (www.solgenomics.net)
The columns are similar to the ones in the table above, and these new colums are included

attributes -> gene model name from the references annotation ITAG v2.3
strand -> gene strand
multiple_exons -> empty or 'yes' when the position overlaps more than one gene
CDS_pos -> position of the polymorphism referenced to the start codon.
codon_pos -> position of the polymorphism in the codon (either 1, 2 or 3).
codon.ref -> codon in the reference sequence
aa.ref -> aminoacid in the reference
For each species analyzed:
codon.SLY -> codon in the species tested
aa.SLY -> aminoacid in the species tested

==> Polymorphisms_in_genes.no_effect_calculated.csv <==
These are polymorphims in coding regions for which the effect could not be calculated (insertions, deletions and heterozygous SNPs) or polymorphisms found in UTRs or introns as indicated by the reference annotation ITAG v2.3 (www.solgenomics.net)
The columns are similar to the tables above.


==> SNPs_in_common_with_potato.csv <==
These are SNPs found in coding regions that match to potato genes in BLAST searches.
The genotype for potato is mentioned in the last column

COLUMNS:

chr -> chromosome from the S. lycopersicum reference genome v 2.40 (www.solgenomics.net)
pos -> position based on chromosomes from the S. lycopersicum reference genome v 2.40 (www.solgenomics.net)
attributes -> gene model name from the references annotation ITAG v2.3
strand -> gene strand
start -> start of the gene
end -> end of the gene
type -> CDS, UTR or intron
kind -> exon or intron
multiple_exons -> empty or 'yes' when the position overlaps more than one gene
CDS_pos -> position of the polymorphism referenced to the start codon.
codon_pos -> position of the polymorphism in the codon (either 1, 2 or 3).
ref -> can be 'INS' for insertions or the reference base from the S. lycopersicum reference genome v 2.40 (www.solgenomics.net)

For each species analyzed:
call.SLY -> the nucleotide call.
freq.SLY -> the frequency of reads containing a similar nucleotide to the nucleotide call. In heterozygous calls the frequency corresponds to the most abundant base
cov.SLY -> Total number of reads overlaping the position, both matching and not matching reads are counted. To calculate the number of reads supporting the nucleotide call multiply this number by the frequency in the previous column.
score.SLY -> quality of the call. It ranges from 0 to 5. A minimum quality of 2 is strongly recommended.

STU -> potato genotype

