Medicago truncatula vs Prunus persica LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) 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: 184,223

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

Uncovered: 355,079,975 out of 412,800,391
Covered: 57,720,416 out of 412,800,391

Uncovered: 14,868,815 out of 50,132,764
Matches: 24,670,538 out of 50,132,764
Mismatches: 9,887,114 out of 50,132,764
Insertions: 706,297 out of 50,132,764

Prunus persica

Uncovered: 179,058,169 out of 227,411,381
Covered: 48,353,212 out of 227,411,381

Uncovered: 5,795,499 out of 33,236,255
Matches: 18,981,372 out of 33,236,255
Mismatches: 7,745,413 out of 33,236,255
Insertions: 713,971 out of 33,236,255

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 persica
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}