Zea mays vs Arabidopsis thaliana LastZ Results

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Zea mays (Zea mays, AGPv3) and Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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: 135,751

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

Uncovered: 2,025,733,928 out of 2,067,864,162
Covered: 42,130,234 out of 2,067,864,162

Uncovered: 20,153,899 out of 44,177,667
Matches: 15,618,287 out of 44,177,667
Mismatches: 7,849,157 out of 44,177,667
Insertions: 556,324 out of 44,177,667

Arabidopsis thaliana

Uncovered: 100,538,948 out of 119,667,750
Covered: 19,128,802 out of 119,667,750

Uncovered: 19,400,362 out of 33,462,323
Matches: 9,140,281 out of 33,462,323
Mismatches: 4,627,948 out of 33,462,323
Insertions: 293,732 out of 33,462,323

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

Zea mays Arabidopsis thaliana
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}