Arabidopsis thaliana vs Eragrostis tef LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Eragrostis tef (Eragrostis tef, ASM97063v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 thalianaEragrostis tef
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 209,632 alignment blocks

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

Uncovered: 86,993,909 out of 119,667,750
Covered: 32,673,841 out of 119,667,750

Uncovered: 13,437,851 out of 33,775,569
Matches: 11,719,768 out of 33,775,569
Mismatches: 8,194,712 out of 33,775,569
Insertions: 423,238 out of 33,775,569
Identity over aligned base-pairs: 57.6%

Eragrostis tef

Uncovered: 544,732,391 out of 607,317,615
Covered: 62,585,224 out of 607,317,615

Uncovered: 18,354,437 out of 47,955,771
Matches: 19,380,263 out of 47,955,771
Mismatches: 9,630,443 out of 47,955,771
Insertions: 590,628 out of 47,955,771
Identity over aligned base-pairs: 65.5%

Block size distribution

Size range All 209,632 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,706
8.8 kb
10 bp - 100 bp
32,198
2.2 Mb
6,665
483.7 kb
100 bp - 1 kb
161,476
53.5 Mb
47,482
19.4 Mb
1 kb - 10 kb
14,252
22.8 Mb
27,498
58.2 Mb
10 kb - 100 kb
40
487.4 kb