Vitis vinifera vs Panicum hallii HAL2 LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Panicum hallii HAL2 (Panicum hallii var. hallii str. HAL2, PhalliiHAL_v2.1) 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: 115,273

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

Uncovered: 451,071,919 out of 486,265,422
Covered: 35,193,503 out of 486,265,422

Uncovered: 10,838,395 out of 32,794,161
Matches: 14,451,586 out of 32,794,161
Mismatches: 7,060,428 out of 32,794,161
Insertions: 443,752 out of 32,794,161

Panicum hallii var. hallii str. HAL2

Uncovered: 465,885,415 out of 487,473,734
Covered: 21,588,319 out of 487,473,734

Uncovered: 22,310,523 out of 37,739,336
Matches: 10,155,667 out of 37,739,336
Mismatches: 4,946,665 out of 37,739,336
Insertions: 326,481 out of 37,739,336

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 Panicum hallii HAL2
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}