Medicago truncatula vs Prunus_dulcis LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Prunus_dulcis (Prunus dulcis, ALMONDv2) 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: 184,917

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

Uncovered: 354,436,906 out of 412,800,391
Covered: 58,363,485 out of 412,800,391

Uncovered: 14,979,626 out of 50,132,764
Matches: 24,529,345 out of 50,132,764
Mismatches: 9,922,079 out of 50,132,764
Insertions: 701,714 out of 50,132,764

Prunus dulcis

Uncovered: 178,044,363 out of 227,498,357
Covered: 49,453,994 out of 227,498,357

Uncovered: 7,109,065 out of 33,980,404
Matches: 18,629,288 out of 33,980,404
Mismatches: 7,534,916 out of 33,980,404
Insertions: 707,135 out of 33,980,404

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 Prunus_dulcis
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options