Medicago truncatula vs Vigna angularis LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Vigna angularis (Vigna angularis, Vigan1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Medicago truncatula 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: 277,593

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 319,442,569 out of 412,800,391
Covered: 93,357,822 out of 412,800,391

Uncovered: 10,637,174 out of 50,132,764
Matches: 29,946,365 out of 50,132,764
Mismatches: 8,697,510 out of 50,132,764
Insertions: 851,715 out of 50,132,764

Vigna angularis

Uncovered: 374,016,953 out of 466,744,453
Covered: 92,727,500 out of 466,744,453

Uncovered: 7,672,875 out of 37,822,470
Matches: 23,250,669 out of 37,822,470
Mismatches: 6,314,411 out of 37,822,470
Insertions: 584,515 out of 37,822,470

Configuration parameters

ParameterValue
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

Medicago truncatula Vigna angularis
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}