Medicago truncatula vs Malus domestica Golden LastZ results
Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Malus domestica Golden (Malus domestica, ASM211411v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. Medicago truncatula 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) | |
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 | Medicago truncatula | Malus domestica Golden |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 10,100,000 | 10,100,000 |
Masking options |
Statistics over 275,664 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Medicago truncatula |
Uncovered: 352,702,896 out of 412,800,391 |
Uncovered: 14,865,978 out of 50,132,764 |
Malus domestica Golden |
Uncovered: 626,043,639 out of 702,961,352 |
Uncovered: 9,052,038 out of 47,560,911 |
Block size distribution
Size range | All 275,664 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 2,858 |
14.6 kb |
|||
10 bp - 100 bp | 45,235 |
3.0 Mb |
13,338 |
962.4 kb |
|
100 bp - 1 kb | 207,763 |
69.4 Mb |
65,247 |
22.3 Mb |
|
1 kb - 10 kb | 19,654 |
31.3 Mb |
24,761 |
61.1 Mb |
|
10 kb - 100 kb | 154 |
3.5 Mb |
937 |
20.0 Mb |
|
100 kb - 1 Mb | 18 |
2.8 Mb |