Medicago truncatula vs Oryza sativa Japonica Group LastZ results
Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Medicago truncatula was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
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 |
Chunking parameters
Parameter | Medicago truncatula | Oryza sativa Japonica Group |
---|---|---|
Chunk size | 20,000,000 | 20,100,000 |
Overlap | 10,000 | 10,000 |
Group set size | 0 | 20,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 147,443 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Medicago truncatula |
Uncovered: 377,376,360 out of 412,800,391 |
Uncovered: 25,211,565 out of 50,132,764 |
Oryza sativa Japonica Group |
Uncovered: 343,863,643 out of 374,424,240 |
Uncovered: 16,015,897 out of 34,124,807 |