Vitis vinifera vs Corchorus capsularis LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Corchorus capsularis (Corchorus capsularis, CCACVL1_1.0) 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: 183,105

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

Uncovered: 425,730,136 out of 486,265,422
Covered: 60,535,286 out of 486,265,422

Uncovered: 3,957,415 out of 32,794,161
Matches: 20,740,618 out of 32,794,161
Mismatches: 7,577,599 out of 32,794,161
Insertions: 518,529 out of 32,794,161

Corchorus capsularis

Uncovered: 267,581,312 out of 317,178,409
Covered: 49,597,097 out of 317,178,409

Uncovered: 6,200,291 out of 30,371,305
Matches: 17,404,145 out of 30,371,305
Mismatches: 6,273,450 out of 30,371,305
Insertions: 493,419 out of 30,371,305

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 Corchorus capsularis
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}