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Arabidopsis thaliana vs Aegilops tauschii LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 thalianaAegilops tauschii
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 155,717 alignment blocks

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

Uncovered: 92,972,330 out of 119,667,750
Covered: 26,695,420 out of 119,667,750

Uncovered: 14,152,899 out of 33,775,569
Matches: 12,557,192 out of 33,775,569
Mismatches: 6,660,650 out of 33,775,569
Insertions: 404,828 out of 33,775,569
Identity over aligned base-pairs: 64.0%

Aegilops tauschii

Uncovered: 4,180,237,993 out of 4,224,915,394
Covered: 44,677,401 out of 4,224,915,394

Uncovered: 28,027,899 out of 53,210,770
Matches: 15,976,130 out of 53,210,770
Mismatches: 8,482,045 out of 53,210,770
Insertions: 724,696 out of 53,210,770
Identity over aligned base-pairs: 63.4%

Block size distribution

Size range All 155,717 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
976
5.0 kb
10 bp - 100 bp
25,010
1.7 Mb
7,417
533.5 kb
100 bp - 1 kb
120,112
40.4 Mb
42,549
17.1 Mb
1 kb - 10 kb
9,603
14.3 Mb
19,429
38.4 Mb
10 kb - 100 kb
15
269.4 kb
41
693.9 kb
100 kb - 1 Mb
1
139.6 kb
1
181.7 kb