Oryza sativa Japonica Group vs Eragrostis tef LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Eragrostis tef (Eragrostis tef, ASM97063v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. Oryza sativa Japonica Group 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

ParameterOryza sativa Japonica GroupEragrostis 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 410,789 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 265,075,038 out of 375,049,285
Covered: 109,974,247 out of 375,049,285

Uncovered: 2,976,006 out of 34,424,450
Matches: 21,144,238 out of 34,424,450
Mismatches: 9,421,913 out of 34,424,450
Insertions: 882,293 out of 34,424,450
Identity over aligned base-pairs: 67.2%

Eragrostis tef

Uncovered: 421,416,292 out of 607,317,615
Covered: 185,901,323 out of 607,317,615

Uncovered: 3,966,328 out of 47,955,771
Matches: 34,942,617 out of 47,955,771
Mismatches: 8,360,345 out of 47,955,771
Insertions: 686,481 out of 47,955,771
Identity over aligned base-pairs: 79.4%

Block size distribution

Size range All 410,789 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,733
20.1 kb
10 bp - 100 bp
54,807
3.4 Mb
19,500
1.4 Mb
100 bp - 1 kb
284,437
110.8 Mb
91,631
33.9 Mb
1 kb - 10 kb
67,809
120.4 Mb
39,925
95.0 Mb
10 kb - 100 kb
3
34.4 kb
3,388
94.4 Mb
100 kb - 1 Mb
77
10.1 Mb