Zea mays vs Arabidopsis thaliana LastZ results
Zea mays (Zea mays, B73_RefGen_v4) and Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 85. Zea mays 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
Parameter | Value |
---|---|
Gap open penalty (O) | 400 |
Gap extend penalty (E) | 30 |
HSP threshold (K) | 3000 |
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
Parameter | Zea mays | Arabidopsis thaliana |
---|---|---|
Chunk size | 50,000,000 | 100,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 100,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 139,180 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Zea mays |
Uncovered: 2,091,499,146 out of 2,134,373,047 |
Uncovered: 21,906,852 out of 48,311,124 |
Arabidopsis thaliana |
Uncovered: 100,397,387 out of 119,667,750 |
Uncovered: 19,299,348 out of 33,462,323 |
Block size distribution
Size range | All 139,180 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 774 |
4.1 kb |
|||
10 bp - 100 bp | 22,606 |
1.6 Mb |
6,542 |
491.3 kb |
|
100 bp - 1 kb | 109,542 |
34.1 Mb |
45,072 |
16.5 Mb |
|
1 kb - 10 kb | 6,258 |
9.1 Mb |
14,104 |
27.4 Mb |
|
10 kb - 100 kb | 28 |
432.1 kb |