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Oryza sativa Japonica Group vs Nicotiana attenuata LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Nicotiana attenuata (Nicotiana attenuata, NIATTr2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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
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 GroupNicotiana attenuata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 119,388 alignment blocks

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

Uncovered: 349,211,865 out of 375,049,285
Covered: 25,837,420 out of 375,049,285

Uncovered: 18,465,050 out of 34,818,902
Matches: 10,479,720 out of 34,818,902
Mismatches: 5,525,196 out of 34,818,902
Insertions: 348,936 out of 34,818,902
Identity over aligned base-pairs: 64.1%

Nicotiana attenuata

Uncovered: 2,342,304,767 out of 2,365,682,703
Covered: 23,377,936 out of 2,365,682,703

Uncovered: 23,512,444 out of 37,106,589
Matches: 8,849,725 out of 37,106,589
Mismatches: 4,489,884 out of 37,106,589
Insertions: 254,536 out of 37,106,589
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 119,388 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
737
3.5 kb
10 bp - 100 bp
21,255
1.5 Mb
7,140
512.7 kb
100 bp - 1 kb
92,296
28.0 Mb
32,190
11.7 Mb
1 kb - 10 kb
5,095
7.7 Mb
12,526
24.8 Mb
10 kb - 100 kb
5
133.8 kb
27
428.3 kb