Single Nucleotide Polymorphisms (SNPs) identified from the whole genome sequences of hilsa shad (Tenualosa ilisha) of the Bay of Bengal

The data file contains 792,939 isolated SNPs identified by discoSnp++ v2.3.x (Uricaru et al., 2015) from the whole genome sequence of T. ilisha of the Bay of Bengal. The central sequence of length 2k-1 is seen in upper case, while the flanking sequences are seen in lower case. SNP_higher/lower: one of the two alleles. id: id of the SNP (each SNP has a unique id).

FOR SNPs:

P_i:pos_Alt1/Alt2: Information about a ith SNP (If more than a unique SNP is found, the following format is used: P_1:pos_Alt1/Alt2,P_2:pos_Alt1/Alt2,...

pos: position of the SNP with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.

Alt1: One of the two alleles

Alt2: the other

FOR INDELs:

P_1:pos_size_repeatSize

pos: predicted position of the indel with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.

size: predicted size of the indel

repeatSize: Size of the longest sequence both prefix of the indel and prefix of the sequence located just after the insertion.

high/low: sequence complexity. If the sequence if of low complexity (e.g. ATATATATATATATAT) this variable would be low

nb_pol: number of polymorphism.

left_unitig_length: size of the full left extension.

right_unitig_length: size of the right extension.

left_contig_length: size of the full left extension.

right_contig_length: size of the right extension.

C1: number of reads mapping the central upper case sequence from the first read set.

C2: number of reads mapping the central upper case sequence from the second read set.

Q1 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the first read set.

Q2 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the second read set.

G1: Genotype of the variant in the first read set.

G2: Genotype of the variant in the second read set.

rank: ranks the predictions according to their read coverage in each condition favoring SNPs that are discriminant between conditions.