Vitis vinifera vs Arabidopsis halleri LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera, Ahal2.2) 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: 169,393

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

Uncovered: 441,514,216 out of 486,265,422
Covered: 44,751,206 out of 486,265,422

Uncovered: 7,610,881 out of 32,794,161
Matches: 16,857,072 out of 32,794,161
Mismatches: 7,695,407 out of 32,794,161
Insertions: 630,801 out of 32,794,161

Arabidopsis halleri subsp. gemmifera

Uncovered: 156,640,131 out of 196,243,198
Covered: 39,603,067 out of 196,243,198

Uncovered: 12,167,693 out of 38,698,211
Matches: 17,982,649 out of 38,698,211
Mismatches: 8,009,981 out of 38,698,211
Insertions: 537,888 out of 38,698,211

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 Arabidopsis halleri
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}