Medicago truncatula vs Malus domestica LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Malus domestica (Malus domestica, ASM211411v1) 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: 276,727

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

Uncovered: 352,562,053 out of 412,800,391
Covered: 60,238,338 out of 412,800,391

Uncovered: 14,839,054 out of 50,132,764
Matches: 24,251,472 out of 50,132,764
Mismatches: 10,272,800 out of 50,132,764
Insertions: 769,438 out of 50,132,764

Malus domestica

Uncovered: 623,660,119 out of 702,961,352
Covered: 79,301,233 out of 702,961,352

Uncovered: 7,731,010 out of 47,560,911
Matches: 27,712,804 out of 47,560,911
Mismatches: 11,115,021 out of 47,560,911
Insertions: 1,002,076 out of 47,560,911

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