Solanum lycopersicum vs Actinidia chinensis Red5 LastZ Results

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Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Actinidia chinensis Red5 (Actinidia chinensis var. chinensis, Red5_PS1_1.69.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Solanum lycopersicum 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: 168,215

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum

Uncovered: 766,948,284 out of 827,747,456
Covered: 60,799,172 out of 827,747,456

Uncovered: 7,417,761 out of 36,416,191
Matches: 20,409,975 out of 36,416,191
Mismatches: 8,041,300 out of 36,416,191
Insertions: 547,155 out of 36,416,191

Actinidia chinensis var. chinensis

Uncovered: 513,238,456 out of 553,842,477
Covered: 40,604,021 out of 553,842,477

Uncovered: 20,842,706 out of 42,227,027
Matches: 15,146,151 out of 42,227,027
Mismatches: 5,789,225 out of 42,227,027
Insertions: 448,945 out of 42,227,027

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

Solanum lycopersicum Actinidia chinensis Red5
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}