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Arabidopsis thaliana vs Oryza nivara LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Arabidopsis thaliana 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

ParameterArabidopsis thalianaOryza nivara
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 111,745 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,487,725 out of 119,667,750
Covered: 26,180,025 out of 119,667,750

Uncovered: 14,486,009 out of 33,775,569
Matches: 12,472,231 out of 33,775,569
Mismatches: 6,434,479 out of 33,775,569
Insertions: 382,850 out of 33,775,569
Identity over aligned base-pairs: 64.7%

Oryza nivara

Uncovered: 309,271,453 out of 337,950,324
Covered: 28,678,871 out of 337,950,324

Uncovered: 22,454,695 out of 42,562,444
Matches: 12,898,391 out of 42,562,444
Mismatches: 6,708,266 out of 42,562,444
Insertions: 501,092 out of 42,562,444
Identity over aligned base-pairs: 64.1%

Block size distribution

Size range All 111,745 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
916
4.7 kb
10 bp - 100 bp
17,146
1.2 Mb
2,792
200.8 kb
100 bp - 1 kb
87,194
29.1 Mb
21,377
9.0 Mb
1 kb - 10 kb
6,486
9.5 Mb
14,484
30.1 Mb
10 kb - 100 kb
3
68.0 kb
38
499.2 kb