| sample |
one individual to be sequenced (human, fish, mouse, bird, etc.) |
| sample library |
all reads produced in a given sequence run for a single sample |
| run library |
all reads produced by a single sequencing run (includes all samples) |
| read |
individual, non-unique sequence produced during sequencing corresponding to the sequence of a single PCR amplicon |
| sequence |
unique read produced during a sequencing run (many reads can correspond to the same sequence), and indicated by an # (e.g. #130) |
| true allele |
sequence inferred to match an allelic sequence in the genome of a given sample |
| artifact |
sequence inferred to not match an allelic sequence in the genome of a given sample |
| cluster |
group of similar reads (or a single read) produced during phase 3 of STC |
| dominant sequence |
sequence with most reads in a given cluster |
| subdominant sequence |
sequence with second most reads in a given cluster |
| dropped allele |
an allele originating from a small cluster in phase 3 that was made a true allele during phase 4 |
| missing allele |
an allele present in the genome of the sample does not appear as a true allele after STC is complete |
