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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
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 thalianaNicotiana attenuata
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 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: 13,404,087 out of 33,775,569
Matches: 13,547,296 out of 33,775,569
Mismatches: 6,374,654 out of 33,775,569
Insertions: 449,532 out of 33,775,569
Identity over aligned base-pairs: 66.5%

Nicotiana attenuata

Uncovered: 1,463,630,138 out of 1,492,146,380
Covered: 28,516,242 out of 1,492,146,380

Uncovered: 7,293,516 out of 23,314,391
Matches: 10,729,058 out of 23,314,391
Mismatches: 4,886,087 out of 23,314,391
Insertions: 405,730 out of 23,314,391
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