Zea mays vs Physcomitrella patens LastZ Results

Back to all analyses

Zea mays (Zea mays, B73_RefGen_v4) and Physcomitrella patens (Physcomitrella patens, Phypa_V3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Zea mays 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: 118,912

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 2,116,207,448 out of 2,135,083,061
Covered: 18,875,613 out of 2,135,083,061

Uncovered: 34,671,752 out of 48,442,923
Matches: 8,800,904 out of 48,442,923
Mismatches: 4,669,959 out of 48,442,923
Insertions: 300,308 out of 48,442,923

Physcomitrella patens

Uncovered: 455,191,909 out of 471,852,792
Covered: 16,660,883 out of 471,852,792

Uncovered: 22,124,677 out of 34,318,961
Matches: 7,847,901 out of 34,318,961
Mismatches: 4,076,785 out of 34,318,961
Insertions: 269,598 out of 34,318,961

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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

Zea mays Physcomitrella patens
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}