Hordeum vulgare vs Triticum aestivum LastZ Results
Back to all analyses
Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) and Triticum aestivum (Triticum aestivum, IWGSC) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Hordeum vulgare was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.
Results
Number of alignment blocks: 6,002,378
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Hordeum vulgare subsp. vulgare |
Uncovered: 3,691,532,476 out of 4,833,907,081 |
Uncovered: 1,616,305 out of 44,392,268 |
Triticum aestivum |
Uncovered: 11,452,554,775 out of 14,547,261,565 |
Uncovered: 5,314,235 out of 136,655,258 |
Configuration parameters
Parameter | Value |
---|---|
Gap open penalty (O) | |
Gap extend penalty (E) | |
HSP threshold (K) | |
Threshold for gapped extension (L) | |
Threshold for alignments between gapped alignment blocks (H) | |
Masking count (M) | |
Seed and Transition value (T) | |
Scoring matrix (Q) | Default: A C G T 91 -114 -31 -123 -114 100 -125 -31 -31 -125 100 -114 -123 -31 -114 91 |
Other parameters (other) | --hspthresh=3000 --inner=2200 --ambiguous=iupac |
Chunking parameters
Hordeum vulgare | Triticum aestivum | |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |