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Oryza sativa Japonica Group vs Arabidopsis halleri LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera, Ahal2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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)
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 GroupArabidopsis halleri
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 122,843 alignment blocks

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

Uncovered: 344,856,627 out of 375,049,285
Covered: 30,192,658 out of 375,049,285

Uncovered: 15,792,351 out of 34,403,043
Matches: 11,868,412 out of 34,403,043
Mismatches: 6,278,757 out of 34,403,043
Insertions: 463,523 out of 34,403,043
Identity over aligned base-pairs: 63.8%

Arabidopsis halleri

Uncovered: 167,241,843 out of 196,243,198
Covered: 29,001,355 out of 196,243,198

Uncovered: 18,384,834 out of 38,698,211
Matches: 13,188,664 out of 38,698,211
Mismatches: 6,724,393 out of 38,698,211
Insertions: 400,320 out of 38,698,211
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 122,843 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
944
4.8 kb
10 bp - 100 bp
18,926
1.3 Mb
3,533
255.3 kb
100 bp - 1 kb
95,783
31.7 Mb
25,324
10.5 Mb
1 kb - 10 kb
7,184
10.8 Mb
15,748
32.6 Mb
10 kb - 100 kb
6
72.9 kb
44
559.7 kb