Vitis vinifera vs Manihot esculenta LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Manihot esculenta (Manihot esculenta, Manihot_esculenta_v6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 258,475

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 407,605,753 out of 486,265,422
Covered: 78,659,669 out of 486,265,422

Uncovered: 3,332,126 out of 32,794,161
Matches: 21,044,388 out of 32,794,161
Mismatches: 7,892,335 out of 32,794,161
Insertions: 525,312 out of 32,794,161

Manihot esculenta

Uncovered: 491,763,147 out of 582,117,524
Covered: 90,354,377 out of 582,117,524

Uncovered: 3,355,332 out of 38,679,430
Matches: 25,616,380 out of 38,679,430
Mismatches: 9,050,509 out of 38,679,430
Insertions: 657,209 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

Vitis vinifera 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}