Zea mays vs Physcomitrella patens LastZ Results

Back to all analyses

Zea mays (Zea mays, AGPv4) and Physcomitrella patens (Physcomitrella patens, ASM242v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 81. 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: 118,723

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

Uncovered: 2,108,569,850 out of 2,134,373,047
Covered: 25,803,197 out of 2,134,373,047

Uncovered: 30,491,963 out of 48,311,124
Matches: 11,449,832 out of 48,311,124
Mismatches: 6,000,994 out of 48,311,124
Insertions: 368,335 out of 48,311,124

Physcomitrella patens

Uncovered: 468,275,089 out of 479,985,347
Covered: 11,710,258 out of 479,985,347

Uncovered: 26,380,187 out of 34,827,652
Matches: 5,406,210 out of 34,827,652
Mismatches: 2,838,514 out of 34,827,652
Insertions: 202,741 out of 34,827,652

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}