Oryza sativa Japonica Group vs Populus trichocarpa LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Populus trichocarpa (Populus trichocarpa, Pop_tri_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 GroupPopulus trichocarpa
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 172,508 alignment blocks

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

Uncovered: 341,608,549 out of 375,049,285
Covered: 33,440,736 out of 375,049,285

Uncovered: 14,278,952 out of 34,403,043
Matches: 13,008,858 out of 34,403,043
Mismatches: 6,656,466 out of 34,403,043
Insertions: 458,767 out of 34,403,043
Identity over aligned base-pairs: 64.6%

Populus trichocarpa

Uncovered: 391,521,029 out of 434,132,815
Covered: 42,611,786 out of 434,132,815

Uncovered: 18,836,544 out of 48,383,886
Matches: 19,287,175 out of 48,383,886
Mismatches: 9,633,692 out of 48,383,886
Insertions: 626,475 out of 48,383,886
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 172,508 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,429
7.1 kb
10 bp - 100 bp
27,113
1.9 Mb
5,274
377.1 kb
100 bp - 1 kb
134,963
43.7 Mb
34,709
13.9 Mb
1 kb - 10 kb
9,002
13.3 Mb
20,461
43.6 Mb
10 kb - 100 kb
1
12.1 kb
70
978.6 kb