Arabidopsis thaliana vs Panicum hallii FIL2 LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Panicum hallii FIL2 (Panicum hallii str. FIL2, PHallii_v3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 77,499

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,830,182 out of 119,667,750
Covered: 25,837,568 out of 119,667,750

Uncovered: 14,382,632 out of 33,775,569
Matches: 12,625,456 out of 33,775,569
Mismatches: 6,402,125 out of 33,775,569
Insertions: 365,356 out of 33,775,569

Panicum hallii str. FIL2

Uncovered: 517,261,402 out of 535,889,049
Covered: 18,627,647 out of 535,889,049

Uncovered: 25,220,505 out of 38,415,885
Matches: 8,560,310 out of 38,415,885
Mismatches: 4,330,664 out of 38,415,885
Insertions: 304,406 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

Arabidopsis thaliana 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}