Arabidopsis thaliana vs Triticum urartu LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Triticum urartu (Triticum urartu, ASM34745v1) 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 thalianaTriticum urartu
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 136,892 alignment blocks

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

Uncovered: 93,686,702 out of 119,667,750
Covered: 25,981,048 out of 119,667,750

Uncovered: 15,349,787 out of 33,775,569
Matches: 11,422,270 out of 33,775,569
Mismatches: 6,642,613 out of 33,775,569
Insertions: 360,899 out of 33,775,569
Identity over aligned base-pairs: 62.0%

Triticum urartu

Uncovered: 3,710,985,707 out of 3,747,163,292
Covered: 36,177,585 out of 3,747,163,292

Uncovered: 18,605,657 out of 36,194,921
Matches: 11,290,792 out of 36,194,921
Mismatches: 5,899,582 out of 36,194,921
Insertions: 398,890 out of 36,194,921
Identity over aligned base-pairs: 64.2%

Block size distribution

Size range All 136,892 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
939
4.8 kb
10 bp - 100 bp
22,087
1.6 Mb
5,559
411.6 kb
100 bp - 1 kb
106,046
34.8 Mb
38,489
15.1 Mb
1 kb - 10 kb
7,807
12.0 Mb
16,257
32.2 Mb
10 kb - 100 kb
13
182.1 kb
48
745.3 kb