Medicago truncatula vs Lupinus angustifolius LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_v1.0) 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: 441,665

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

Uncovered: 316,581,519 out of 412,800,391
Covered: 96,218,872 out of 412,800,391

Uncovered: 10,891,015 out of 50,132,764
Matches: 29,919,995 out of 50,132,764
Mismatches: 8,458,775 out of 50,132,764
Insertions: 862,979 out of 50,132,764

Lupinus angustifolius

Uncovered: 465,716,336 out of 609,203,021
Covered: 143,486,685 out of 609,203,021

Uncovered: 1,036,221 out of 18,016,600
Matches: 13,359,719 out of 18,016,600
Mismatches: 3,261,951 out of 18,016,600
Insertions: 358,709 out of 18,016,600

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 Lupinus angustifolius
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}