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Oryza sativa Japonica Group vs Physcomitrium patens LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Physcomitrium patens (Physcomitrium 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
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 GroupPhyscomitrium patens
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size100,100,000
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: 22,404,062 out of 34,818,902
Matches: 7,889,420 out of 34,818,902
Mismatches: 4,262,206 out of 34,818,902
Insertions: 263,214 out of 34,818,902
Identity over aligned base-pairs: 63.5%

Physcomitrium patens

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

Uncovered: 22,573,045 out of 35,713,650
Matches: 8,453,847 out of 35,713,650
Mismatches: 4,396,546 out of 35,713,650
Insertions: 290,212 out of 35,713,650
Identity over aligned base-pairs: 64.3%

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