Medicago truncatula vs Lupinus angustifolius LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_v1.0) 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: 445,766

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

Uncovered: 316,466,329 out of 412,800,391
Covered: 96,334,062 out of 412,800,391

Uncovered: 10,881,598 out of 50,132,764
Matches: 29,926,035 out of 50,132,764
Mismatches: 8,461,897 out of 50,132,764
Insertions: 863,234 out of 50,132,764

Lupinus angustifolius

Uncovered: 464,158,752 out of 609,203,021
Covered: 145,044,269 out of 609,203,021

Uncovered: 2,186,065 out of 42,631,353
Matches: 31,817,994 out of 42,631,353
Mismatches: 7,777,922 out of 42,631,353
Insertions: 849,372 out of 42,631,353

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 Lupinus angustifolius
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}