Vitis vinifera vs Marchantia polymorpha LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Marchantia polymorpha (Marchantia polymorpha str. Tak-1, Marchanta_polymorpha_v1) 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: 85,039

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

Uncovered: 468,576,503 out of 486,265,422
Covered: 17,688,919 out of 486,265,422

Uncovered: 20,080,431 out of 32,794,161
Matches: 8,122,335 out of 32,794,161
Mismatches: 4,390,621 out of 32,794,161
Insertions: 200,774 out of 32,794,161

Marchantia polymorpha str. Tak-1

Uncovered: 214,368,456 out of 225,760,816
Covered: 11,392,360 out of 225,760,816

Uncovered: 15,267,310 out of 23,498,831
Matches: 5,237,752 out of 23,498,831
Mismatches: 2,805,485 out of 23,498,831
Insertions: 188,284 out of 23,498,831

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 Marchantia polymorpha
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}