Medicago truncatula vs Vitis vinifera LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Vitis vinifera (Vitis vinifera, 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 were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterMedicago truncatulaVitis vinifera
Chunk size20,000,00020,100,000
Group set size020,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 245,816 alignment blocks

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

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
Identity over aligned base-pairs: 69.1%

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
Identity over aligned base-pairs: 69.6%