Zea mays vs Vitis vinifera LastZ Results

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Zea mays (Zea mays, AGPv4) and Vitis vinifera (Vitis vinifera, IGGP_12x) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 81. Zea mays 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: 164,740

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 2,087,384,281 out of 2,134,373,047
Covered: 46,988,766 out of 2,134,373,047

Uncovered: 18,656,633 out of 48,311,124
Matches: 19,534,860 out of 48,311,124
Mismatches: 9,431,260 out of 48,311,124
Insertions: 688,371 out of 48,311,124

Vitis vinifera

Uncovered: 422,264,897 out of 443,044,434
Covered: 20,779,537 out of 443,044,434

Uncovered: 16,099,416 out of 30,493,931
Matches: 9,515,767 out of 30,493,931
Mismatches: 4,560,494 out of 30,493,931
Insertions: 318,254 out of 30,493,931

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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

Zea mays Vitis vinifera
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}