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Arabidopsis thaliana vs Nicotiana attenuata LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Nicotiana attenuata (Nicotiana attenuata, NIATTr2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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
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

ParameterArabidopsis thalianaNicotiana 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 119,466 alignment blocks

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

Uncovered: 91,979,946 out of 119,667,750
Covered: 27,687,804 out of 119,667,750

Uncovered: 13,404,236 out of 33,775,569
Matches: 13,547,196 out of 33,775,569
Mismatches: 6,374,591 out of 33,775,569
Insertions: 449,546 out of 33,775,569
Identity over aligned base-pairs: 66.5%

Nicotiana attenuata

Uncovered: 2,337,166,461 out of 2,365,682,703
Covered: 28,516,242 out of 2,365,682,703

Uncovered: 21,085,716 out of 37,106,589
Matches: 10,729,066 out of 37,106,589
Mismatches: 4,886,078 out of 37,106,589
Insertions: 405,729 out of 37,106,589
Identity over aligned base-pairs: 67.0%

Block size distribution

Size range All 119,466 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
820
4.5 kb
10 bp - 100 bp
19,587
1.3 Mb
6,128
439.5 kb
100 bp - 1 kb
92,252
30.0 Mb
28,722
10.8 Mb
1 kb - 10 kb
6,801
10.2 Mb
14,444
29.9 Mb
10 kb - 100 kb
6
157.2 kb
36
561.9 kb