Vitis vinifera vs Panicum hallii FIL2 LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Panicum hallii FIL2 (Panicum hallii str. FIL2, PHallii_v3.1) 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: 115,151

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

Uncovered: 450,794,718 out of 486,265,422
Covered: 35,470,704 out of 486,265,422

Uncovered: 10,799,283 out of 32,794,161
Matches: 14,441,571 out of 32,794,161
Mismatches: 7,107,880 out of 32,794,161
Insertions: 445,427 out of 32,794,161

Panicum hallii str. FIL2

Uncovered: 514,369,728 out of 535,889,049
Covered: 21,519,321 out of 535,889,049

Uncovered: 23,048,467 out of 38,415,885
Matches: 10,126,036 out of 38,415,885
Mismatches: 4,915,545 out of 38,415,885
Insertions: 325,837 out of 38,415,885

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 FIL2
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}