Oryza sativa Japonica Group vs Physcomitrella patens LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Physcomitrella patens (Physcomitrella patens, Phypa_V3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterOryza sativa Japonica GroupPhyscomitrella patens
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 111,420 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 357,025,229 out of 375,049,285
Covered: 18,024,056 out of 375,049,285

Uncovered: 22,169,182 out of 34,403,043
Matches: 7,773,821 out of 34,403,043
Mismatches: 4,200,564 out of 34,403,043
Insertions: 259,476 out of 34,403,043
Identity over aligned base-pairs: 63.5%

Physcomitrella patens

Uncovered: 453,957,387 out of 471,852,792
Covered: 17,895,405 out of 471,852,792

Uncovered: 21,364,479 out of 34,318,961
Matches: 8,339,146 out of 34,318,961
Mismatches: 4,334,048 out of 34,318,961
Insertions: 281,288 out of 34,318,961
Identity over aligned base-pairs: 64.4%

Block size distribution

Size range All 111,420 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
915
4.6 kb
10 bp - 100 bp
23,277
1.7 Mb
3,338
238.1 kb
100 bp - 1 kb
85,069
23.5 Mb
22,750
9.6 Mb
1 kb - 10 kb
2,159
2.9 Mb
9,621
18.1 Mb
10 kb - 100 kb
11
124.2 kb