Medicago truncatula vs Arabidopsis lyrata LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) 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: 164,143

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

Uncovered: 367,330,608 out of 412,800,391
Covered: 45,469,783 out of 412,800,391

Uncovered: 20,212,664 out of 50,132,764
Matches: 19,888,563 out of 50,132,764
Mismatches: 9,258,455 out of 50,132,764
Insertions: 773,082 out of 50,132,764

Arabidopsis lyrata subsp. lyrata

Uncovered: 167,532,744 out of 206,667,935
Covered: 39,135,191 out of 206,667,935

Uncovered: 10,006,827 out of 35,389,059
Matches: 16,998,254 out of 35,389,059
Mismatches: 7,798,497 out of 35,389,059
Insertions: 585,481 out of 35,389,059

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 Arabidopsis lyrata
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}