Arabidopsis thaliana vs Glycine max LastZ Results
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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Glycine max (Glycine max, Glycine_max_v2.0) 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: 263,333
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Arabidopsis thaliana |
Uncovered: 82,669,201 out of 119,667,750 |
Uncovered: 8,427,625 out of 33,775,569 |
Glycine max |
Uncovered: 898,339,146 out of 978,416,860 |
Uncovered: 17,495,021 out of 65,631,894 |
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 | Glycine max | |
---|---|---|
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} |