Arabidopsis thaliana vs Physcomitrella patens LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Physcomitrella patens (Physcomitrella patens, ASM242v1) 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: 99,351

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

Uncovered: 102,948,997 out of 119,667,750
Covered: 16,718,753 out of 119,667,750

Uncovered: 21,106,332 out of 33,775,569
Matches: 8,066,869 out of 33,775,569
Mismatches: 4,366,177 out of 33,775,569
Insertions: 236,191 out of 33,775,569

Physcomitrella patens

Uncovered: 461,476,935 out of 479,985,347
Covered: 18,508,412 out of 479,985,347

Uncovered: 21,950,950 out of 34,827,652
Matches: 8,243,765 out of 34,827,652
Mismatches: 4,343,222 out of 34,827,652
Insertions: 289,715 out of 34,827,652

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 Physcomitrella patens
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}