Medicago truncatula vs Vitis vinifera LastZ Results

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Medicago truncatula (Medicago truncatula str. A17, MedtrA17_4.0) and Vitis vinifera (Vitis vinifera, IGGP_12x) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. 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: 245,816

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula str. A17

Uncovered: 353,455,675 out of 412,800,391
Covered: 59,344,716 out of 412,800,391

Uncovered: 13,405,185 out of 50,132,764
Matches: 25,386,187 out of 50,132,764
Mismatches: 10,590,550 out of 50,132,764
Insertions: 750,842 out of 50,132,764

Vitis vinifera

Uncovered: 419,698,802 out of 486,265,422
Covered: 66,566,620 out of 486,265,422

Uncovered: 4,738,701 out of 32,794,161
Matches: 19,529,429 out of 32,794,161
Mismatches: 7,913,392 out of 32,794,161
Insertions: 612,639 out of 32,794,161

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 Vitis vinifera
Chunk size 20,000,000 20,100,000
Overlap 10,000 10,000
Group set size 0 20,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}