Medicago truncatula vs Phaseolus vulgaris LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Phaseolus vulgaris (Phaseolus vulgaris, PhaVulg1_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: 288,768

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

Uncovered: 316,448,526 out of 412,800,391
Covered: 96,351,865 out of 412,800,391

Uncovered: 10,475,191 out of 50,132,764
Matches: 30,054,350 out of 50,132,764
Mismatches: 8,742,729 out of 50,132,764
Insertions: 860,494 out of 50,132,764

Phaseolus vulgaris

Uncovered: 418,133,900 out of 521,076,696
Covered: 102,942,796 out of 521,076,696

Uncovered: 2,242,829 out of 34,663,348
Matches: 25,105,215 out of 34,663,348
Mismatches: 6,689,286 out of 34,663,348
Insertions: 626,018 out of 34,663,348

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 Phaseolus vulgaris
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}