Table 1. Output of SnpEff.
| # SNP |
Gene_name |
Effect |
Old_AA/new_AA |
Old_codon/New_codon |
Codon_Num (CDS) |
CDS_size |
| chr2L:10006682_C/T |
CG31755 |
UPSTREAM: 541 bases |
|
|
|
|
| chr2L:10006758_G/A |
CG31755 |
UPSTREAM:465 bases |
|
|
|
|
| chr2L:10007289_G/A |
CG4747 |
SYNONYMOUS_CODING |
L/L |
TTG/TTA |
489 |
1809 |
| chr2L:10007319_G/C |
CG4747 |
SYNONYMOUS_CODING |
G/G |
GGG/GGC |
499 |
1809 |
| chr2L:10007356_A/T |
CG4747 |
INTRON |
|
|
|
1809 |
| chr2L:10007363_T/A | CG4747 | INTRON | 1809 |
#
SNP, a description of the single nucleotide polymorphism (SNP) indicating chromosome arm (chr2L), coordinate in genome (10006682), and nucleotide change (e.g., C/T indicates that C is replaced by T in w1118; iso-2; iso-3 at this position). Gene_name, official gene symbol of gene. Effect, description of SNP (e.g., upstream of transcription start site at position -541). Old_AA/new/AA, amino acid change, if any, in one letter code. Old_codon/New_codon, if a codon contains a SNP, the old (reference) and new (w1118; iso-2; iso-3) codons are indicated. Codon_Num(CDS), the codon number of the coding sequence (CDS). CDS_size, the size of the protein in amino acids.