For example, a recent study on Sarcin-Ricin internal loop motif (SR-motif) reports two structurally observed variants of the reference native SR-motif (variant 0), characterized by isosteric substitutions of two different A G H S Trans base pairs, respectively.
the program calculates additional features such as the number of bases to the closest variant, mean and standard deviation of the entropy of the genotype distribution across all samples of the variant, entropy of the reference sequence near the variant.
However, the average imputation confidence (INFO score) is considerably lower for rare variants than for common variants, irrespective of the reference panel.
To overcome these limitations, the NIST-led "Genome in a Bottle" Consortium (NIST-GIAB) [ 20] developed a community resource of high-confidence variants for the reference individual NA12878.
For annotation of the variants, version 5b60 of the reference sequence B73 AGP_v2 was used (ftp://ftp.gramene.org/pub/gramene/maizesequence.org/release-5b/filtered-set/) which contains 39,656 gene models.
All SNPs were identified as variants of the JGI reference so n/a denotes that SNPs unique to comparisons between transcriptomes could not be identified.
The presence of paralogous genes and isoforms from splice variants, and quality of the reference sequences could contribute to the observed duplicate mapping [ 39– 41] and some 454 reads mapping to multiple sites may represent transcribed transposable elements.
The Integrative Genomics Viewer (IGV) (Thorvaldsdottir et al, 2012) was used to visualise the read alignment and the presence of variants against the reference genome as well as to confirm variant calls by checking for strand biases and sequencing errors.
Imputation-based genomic coverage is calculated as the number of imputed variants with quality scores above the threshold value (info score ≥ 0.8) divided by the total number of variants in the reference panel [ 24].
Comparisons of the same ∼10.15 Mb region in human and chimpanzee Y chromosomes identified 21,278 A-T/234,420 total mutations, and comparisons of variants between the reference sequence and all filtered SNPs in the individual we sequenced identified 46 A-T/629 total mutations.
