Medicago truncatula vs Manihot esculenta LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Manihot esculenta (Manihot esculenta, Manihot_esculenta_v6) 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: 224,714

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

Uncovered: 349,392,271 out of 412,800,391
Covered: 63,408,120 out of 412,800,391

Uncovered: 14,900,418 out of 50,132,764
Matches: 24,071,656 out of 50,132,764
Mismatches: 10,416,141 out of 50,132,764
Insertions: 744,549 out of 50,132,764

Manihot esculenta

Uncovered: 515,672,130 out of 582,117,524
Covered: 66,445,394 out of 582,117,524

Uncovered: 5,639,729 out of 38,679,430
Matches: 22,923,607 out of 38,679,430
Mismatches: 9,304,188 out of 38,679,430
Insertions: 811,906 out of 38,679,430

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 Manihot esculenta
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}