Arabidopsis thaliana vs Triticum dicoccoides LastZ Results
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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 359,368
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Arabidopsis thaliana |
Uncovered: 91,559,711 out of 119,667,750 |
Uncovered: 13,622,876 out of 33,775,569 |
Triticum dicoccoides |
Uncovered: 9,963,479,210 out of 10,079,039,394 |
Uncovered: 54,144,821 out of 100,651,268 |
Configuration parameters
Parameter | Value |
---|---|
Gap open penalty (O) | 400 |
Gap extend penalty (E) | 30 |
HSP threshold (K) | |
Threshold for gapped extension (L) | 3000 |
Threshold for alignments between gapped alignment blocks (H) | 2200 |
Masking count (M) | |
Seed and Transition value (T) | 1 |
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) | --ambiguous=iupac |
Chunking parameters
Arabidopsis thaliana | Triticum dicoccoides | |
---|---|---|
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} |