Vitis vinifera vs Nicotiana attenuata LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Nicotiana attenuata (Nicotiana attenuata, NIATTr2) 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: 218,979

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

Uncovered: 438,569,948 out of 486,265,422
Covered: 47,695,474 out of 486,265,422

Uncovered: 9,277,381 out of 32,794,161
Matches: 16,143,415 out of 32,794,161
Mismatches: 6,897,612 out of 32,794,161
Insertions: 475,753 out of 32,794,161

Nicotiana attenuata

Uncovered: 1,435,622,376 out of 1,492,146,380
Covered: 56,524,004 out of 1,492,146,380

Uncovered: 4,791,913 out of 23,314,391
Matches: 13,037,905 out of 23,314,391
Mismatches: 5,140,177 out of 23,314,391
Insertions: 344,396 out of 23,314,391

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 Nicotiana attenuata
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}