Medicago truncatula vs Brassica rapa LastZ Results

Back to all analyses

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Brassica rapa (Brassica rapa, Brapa_1.0) 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: 219,989

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

Uncovered: 367,287,657 out of 412,800,391
Covered: 45,512,734 out of 412,800,391

Uncovered: 20,425,142 out of 50,132,764
Matches: 19,573,165 out of 50,132,764
Mismatches: 9,278,111 out of 50,132,764
Insertions: 856,346 out of 50,132,764

Brassica rapa

Uncovered: 229,542,177 out of 283,822,783
Covered: 54,280,606 out of 283,822,783

Uncovered: 13,295,301 out of 48,055,850
Matches: 23,337,735 out of 48,055,850
Mismatches: 10,667,482 out of 48,055,850
Insertions: 755,332 out of 48,055,850

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 Brassica rapa
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}