LORA Report
Report created with LORA (v1.0.1)
The table below shows key assembly statistics for each sample, including contig counts, assembly size, read mapping rate, and BUSCO completeness scores where available. Click on any row to display the detailed per-sample results in the sections below.
| Sample | # contigs | Largest contig | Total length | Mapped (%) | Avg. coverage depth | Complete BUSCOs | Complete and duplicated BUSCOs | Fragmented BUSCOs | Missing BUSCOs |
|---|---|---|---|---|---|---|---|---|---|
| hifi | 2 | 2205694 | 2218423 | 100.0 | 113 | 123 | 0 | 1 | 0 |
| hifi2 | 2 | 2205964 | 2218693 | 100.0 | 83 | 123 | 0 | 1 | 0 |
| hifi3 | 2 | 2205694 | 2218423 | 100.0 | 66 | 123 | 0 | 1 | 0 |
| hifi4 | 2 | 2205301 | 2218030 | 100.0 | 49 | 123 | 0 | 1 | 0 |
| hifi5 | 2 | 2206873 | 2219602 | 100.0 | 32 | 123 | 0 | 1 | 0 |
Download the final contig sequences for this sample: hifi.fasta.
Assembly graph produced by Bandage showing contig connectivity before circularisation. Hover the image to view it in colour.
BUSCO assesses genome completeness by searching for a set of near-universal single-copy orthologs. Values show counts of complete (single-copy and duplicated), fragmented, and missing BUSCOs.
| Complete BUSCOs | 123 |
|---|---|
| Complete and duplicated BUSCOs | 0 |
| Fragmented BUSCOs | 1 |
| Missing BUSCOs | 0 |
CheckM estimates genome completeness and contamination by placing the assembly in a reference genome tree and identifying lineage-specific marker genes.
| Completeness | 99.61 |
|---|---|
| Contamination | 0.77 |
| Heterogenity | 0.00 |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 2205694 |
|---|---|
| DOC | 112.311 |
| BOC | 100.000 |
| GC (%) | 37.65 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CP119172 | 100.0 | 100000 | 0 | 0 | 1 | 100000 | 2011341 | 1911342 | 0 | 180338.0 | nan | Streptococcus macedonicus strain SGM CIP105683 chromosome, complete genome |
| CP113440 | 99.0 | 35670 | 327 | 9 | 54985 | 90632 | 2067569 | 2031909 | 0 | 62700.8 | nan | Streptococcus macedonicus strain E37 chromosome, complete genome |
| HE613569 | 98.98 | 30916 | 303 | 7 | 59722 | 90632 | 1851596 | 1820689 | 0 | 54309.7 | nan | Streptococcus macedonicus ACA-DC 198 main chromosome complete genome |
| CP013688 | 99.63 | 28179 | 94 | 6 | 62458 | 90632 | 138442 | 166615 | 0 | 50335.1 | nan | Streptococcus gallolyticus strain ICDDRB-NRC-S1 chromosome, complete genome |
| LS483409 | 97.42 | 26704 | 604 | 21 | 63947 | 90575 | 2214427 | 2187735 | 0 | 45030.5 | nan | Streptococcus gallolyticus strain NCTC13773 genome assembly, chromosome: 1 |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 12729 |
|---|---|
| DOC | 80.502 |
| BOC | 100.000 |
| GC (%) | 35.04 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HE613570 | 99.98 | 10963 | 1 | 1 | 1 | 10963 | 10962 | 1 | 0 | 19759.0 | nan | Streptococcus macedonicus ACA-DC 198 plasmid pSMA198, complete genome |
| CP119173 | 99.97 | 9773 | 3 | 0 | 1 | 9773 | 9773 | 1 | 0 | 17612.1 | nan | Streptococcus macedonicus strain SGM CIP105683 plasmid pSMA198, complete sequence |
| CP104046 | 98.67 | 4291 | 53 | 4 | 2521 | 6810 | 902742 | 898455 | 0 | 7468.13 | nan | Streptococcus parauberis strain KSP14 chromosome, complete genome |
| CP104047 | 98.65 | 4292 | 53 | 5 | 2521 | 6810 | 902745 | 898457 | 0 | 7461.82 | nan | Streptococcus parauberis strain KSP10 chromosome, complete genome |
| CP095082 | 98.27 | 3000 | 38 | 3 | 9730 | 12729 | 4261 | 1276 | 0 | 5176.05 | nan | Streptococcus dysgalactiae strain WJ001 plasmid unnamed1, complete sequence |
Download the final contig sequences for this sample: hifi2.fasta.
Assembly graph produced by Bandage showing contig connectivity before circularisation. Hover the image to view it in colour.
BUSCO assesses genome completeness by searching for a set of near-universal single-copy orthologs. Values show counts of complete (single-copy and duplicated), fragmented, and missing BUSCOs.
| Complete BUSCOs | 123 |
|---|---|
| Complete and duplicated BUSCOs | 0 |
| Fragmented BUSCOs | 1 |
| Missing BUSCOs | 0 |
CheckM estimates genome completeness and contamination by placing the assembly in a reference genome tree and identifying lineage-specific marker genes.
| Completeness | 99.61 |
|---|---|
| Contamination | 0.77 |
| Heterogenity | 0.00 |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 2205964 |
|---|---|
| DOC | 82.225 |
| BOC | 100.000 |
| GC (%) | 37.65 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CP119172 | 100.0 | 100000 | 0 | 0 | 1 | 100000 | 2005323 | 1905324 | 0 | 180338.0 | nan | Streptococcus macedonicus strain SGM CIP105683 chromosome, complete genome |
| CP113440 | 99.0 | 35670 | 327 | 9 | 48967 | 84614 | 2067569 | 2031909 | 0 | 62700.8 | nan | Streptococcus macedonicus strain E37 chromosome, complete genome |
| HE613569 | 98.98 | 30916 | 303 | 7 | 53704 | 84614 | 1851596 | 1820689 | 0 | 54309.7 | nan | Streptococcus macedonicus ACA-DC 198 main chromosome complete genome |
| CP013688 | 99.63 | 28179 | 94 | 6 | 56440 | 84614 | 138442 | 166615 | 0 | 50335.1 | nan | Streptococcus gallolyticus strain ICDDRB-NRC-S1 chromosome, complete genome |
| LS483409 | 97.42 | 26704 | 604 | 21 | 57929 | 84557 | 2214427 | 2187735 | 0 | 45030.5 | nan | Streptococcus gallolyticus strain NCTC13773 genome assembly, chromosome: 1 |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 12729 |
|---|---|
| DOC | 62.770 |
| BOC | 100.000 |
| GC (%) | 35.04 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HE613570 | 99.98 | 10963 | 1 | 1 | 1 | 10963 | 10962 | 1 | 0 | 19759.0 | nan | Streptococcus macedonicus ACA-DC 198 plasmid pSMA198, complete genome |
| CP119173 | 99.97 | 9773 | 3 | 0 | 1 | 9773 | 9773 | 1 | 0 | 17612.1 | nan | Streptococcus macedonicus strain SGM CIP105683 plasmid pSMA198, complete sequence |
| CP104046 | 98.67 | 4291 | 53 | 4 | 2521 | 6810 | 902742 | 898455 | 0 | 7468.13 | nan | Streptococcus parauberis strain KSP14 chromosome, complete genome |
| CP104047 | 98.65 | 4292 | 53 | 5 | 2521 | 6810 | 902745 | 898457 | 0 | 7461.82 | nan | Streptococcus parauberis strain KSP10 chromosome, complete genome |
| CP095082 | 98.27 | 3000 | 38 | 3 | 9730 | 12729 | 4261 | 1276 | 0 | 5176.05 | nan | Streptococcus dysgalactiae strain WJ001 plasmid unnamed1, complete sequence |
Download the final contig sequences for this sample: hifi3.fasta.
Assembly graph produced by Bandage showing contig connectivity before circularisation. Hover the image to view it in colour.
BUSCO assesses genome completeness by searching for a set of near-universal single-copy orthologs. Values show counts of complete (single-copy and duplicated), fragmented, and missing BUSCOs.
| Complete BUSCOs | 123 |
|---|---|
| Complete and duplicated BUSCOs | 0 |
| Fragmented BUSCOs | 1 |
| Missing BUSCOs | 0 |
CheckM estimates genome completeness and contamination by placing the assembly in a reference genome tree and identifying lineage-specific marker genes.
| Completeness | 99.61 |
|---|---|
| Contamination | 0.77 |
| Heterogenity | 0.00 |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 2205694 |
|---|---|
| DOC | 65.712 |
| BOC | 100.000 |
| GC (%) | 37.65 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CP119172 | 100.0 | 100000 | 0 | 0 | 1 | 100000 | 1670131 | 1770130 | 0 | 180338.0 | nan | Streptococcus macedonicus strain SGM CIP105683 chromosome, complete genome |
| HE613569 | 99.79 | 70140 | 89 | 7 | 4857 | 74936 | 1604541 | 1674680 | 0 | 125840.0 | nan | Streptococcus macedonicus ACA-DC 198 main chromosome complete genome |
| CP013688 | 99.24 | 53736 | 369 | 16 | 27040 | 80755 | 359435 | 305717 | 0 | 95037.9 | nan | Streptococcus gallolyticus strain ICDDRB-NRC-S1 chromosome, complete genome |
| OZ254910 | 97.13 | 42130 | 1046 | 40 | 6443 | 48417 | 1743198 | 1785317 | 0 | 70486.0 | nan | Streptococcus gallolyticus subsp. gallolyticus isolate 37 genome assembly, chromosome: 1 |
| OZ254908 | 96.95 | 33491 | 886 | 24 | 6443 | 39805 | 1814409 | 1847891 | 0 | 55804.7 | nan | Streptococcus gallolyticus subsp. gallolyticus isolate 30 genome assembly, chromosome: 1 |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 12729 |
|---|---|
| DOC | 49.180 |
| BOC | 100.000 |
| GC (%) | 35.04 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CP119173 | 99.97 | 11046 | 3 | 0 | 1684 | 12729 | 12729 | 1684 | 0 | 19907.8 | nan | Streptococcus macedonicus strain SGM CIP105683 plasmid pSMA198, complete sequence |
| HE613570 | 99.99 | 9856 | 0 | 1 | 2874 | 12729 | 12728 | 2874 | 0 | 17767.2 | nan | Streptococcus macedonicus ACA-DC 198 plasmid pSMA198, complete genome |
| OX461091 | 93.62 | 5531 | 329 | 14 | 1640 | 7159 | 8087 | 2570 | 0 | 8342.77 | nan | Streptococcus agalactiae isolate MRI Z2-336 genome assembly, plasmid: IME |
| MW118671 | 93.62 | 5531 | 329 | 14 | 1640 | 7159 | 8087 | 2570 | 0 | 8342.77 | nan | Streptococcus agalactiae strain MRIZ2-336 integrative mobilizable element mobile element, complete sequence |
| CP125109 | 97.58 | 4709 | 81 | 18 | 1640 | 6335 | 4689 | 1 | 0 | 7927.99 | nan | Streptococcus iniae strain GXAS200705 plasmid unnamed1, complete sequence |
Download the final contig sequences for this sample: hifi4.fasta.
Assembly graph produced by Bandage showing contig connectivity before circularisation. Hover the image to view it in colour.
BUSCO assesses genome completeness by searching for a set of near-universal single-copy orthologs. Values show counts of complete (single-copy and duplicated), fragmented, and missing BUSCOs.
| Complete BUSCOs | 123 |
|---|---|
| Complete and duplicated BUSCOs | 0 |
| Fragmented BUSCOs | 1 |
| Missing BUSCOs | 0 |
CheckM estimates genome completeness and contamination by placing the assembly in a reference genome tree and identifying lineage-specific marker genes.
| Completeness | 99.61 |
|---|---|
| Contamination | 0.77 |
| Heterogenity | 0.00 |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 2205301 |
|---|---|
| DOC | 49.228 |
| BOC | 100.000 |
| GC (%) | 37.65 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CP119172 | 100.0 | 100000 | 0 | 0 | 1 | 100000 | 405085 | 505084 | 0 | 180338.0 | nan | Streptococcus macedonicus strain SGM CIP105683 chromosome, complete genome |
| CP013688 | 99.87 | 39737 | 39 | 3 | 16998 | 56725 | 1552888 | 1513154 | 0 | 71432.7 | nan | Streptococcus gallolyticus strain ICDDRB-NRC-S1 chromosome, complete genome |
| CP113440 | 99.78 | 39728 | 55 | 1 | 16998 | 56725 | 466011 | 505705 | 0 | 71274.0 | nan | Streptococcus macedonicus strain E37 chromosome, complete genome |
| HE613569 | 99.85 | 35085 | 50 | 3 | 21643 | 56725 | 445102 | 480184 | 0 | 63019.1 | nan | Streptococcus macedonicus ACA-DC 198 main chromosome complete genome |
| AP012053 | 97.62 | 21934 | 492 | 11 | 16998 | 38920 | 451924 | 473839 | 0 | 37184.0 | nan | Streptococcus gallolyticus subsp. gallolyticus ATCC 43143 DNA, complete genome |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 12729 |
|---|---|
| DOC | 38.954 |
| BOC | 100.000 |
| GC (%) | 35.04 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HE613570 | 99.98 | 12463 | 1 | 1 | 267 | 12729 | 12728 | 267 | 0 | 22464.0 | nan | Streptococcus macedonicus ACA-DC 198 plasmid pSMA198, complete genome |
| CP119173 | 99.97 | 11805 | 3 | 0 | 1 | 11805 | 11805 | 1 | 0 | 21276.5 | nan | Streptococcus macedonicus strain SGM CIP105683 plasmid pSMA198, complete sequence |
| CP104046 | 98.67 | 4291 | 53 | 4 | 4553 | 8842 | 902742 | 898455 | 0 | 7468.13 | nan | Streptococcus parauberis strain KSP14 chromosome, complete genome |
| CP104047 | 98.65 | 4292 | 53 | 5 | 4553 | 8842 | 902745 | 898457 | 0 | 7461.82 | nan | Streptococcus parauberis strain KSP10 chromosome, complete genome |
| OX461091 | 95.52 | 4554 | 192 | 7 | 1 | 4552 | 7113 | 2570 | 0 | 7273.37 | nan | Streptococcus agalactiae isolate MRI Z2-336 genome assembly, plasmid: IME |
Download the final contig sequences for this sample: hifi5.fasta.
Assembly graph produced by Bandage showing contig connectivity before circularisation. Hover the image to view it in colour.
BUSCO assesses genome completeness by searching for a set of near-universal single-copy orthologs. Values show counts of complete (single-copy and duplicated), fragmented, and missing BUSCOs.
| Complete BUSCOs | 123 |
|---|---|
| Complete and duplicated BUSCOs | 0 |
| Fragmented BUSCOs | 1 |
| Missing BUSCOs | 0 |
CheckM estimates genome completeness and contamination by placing the assembly in a reference genome tree and identifying lineage-specific marker genes.
| Completeness | 99.61 |
|---|---|
| Contamination | 0.77 |
| Heterogenity | 0.00 |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 2206873 |
|---|---|
| DOC | 32.699 |
| BOC | 100.000 |
| GC (%) | 37.66 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CP119172 | 100.0 | 100000 | 0 | 0 | 1 | 100000 | 1449652 | 1549651 | 0 | 180338.0 | nan | Streptococcus macedonicus strain SGM CIP105683 chromosome, complete genome |
| HE613569 | 99.59 | 45158 | 112 | 8 | 54903 | 100000 | 1435382 | 1480526 | 0 | 80633.5 | nan | Streptococcus macedonicus ACA-DC 198 main chromosome complete genome |
| CP013688 | 99.45 | 29053 | 67 | 8 | 65142 | 94101 | 561431 | 532379 | 0 | 51721.0 | nan | Streptococcus gallolyticus strain ICDDRB-NRC-S1 chromosome, complete genome |
| CP072435 | 98.44 | 26348 | 410 | 1 | 20630 | 46976 | 678877 | 652530 | 0 | 45659.9 | nan | Streptococcus thermophilus strain S24736 chromosome, complete genome |
| CP191581 | 97.64 | 22374 | 414 | 22 | 65142 | 87450 | 1542990 | 1565315 | 0 | 37976.6 | nan | Streptococcus gallolyticus strain 202 chromosome, complete genome |
Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.
| length | 12729 |
|---|---|
| DOC | 24.966 |
| BOC | 100.000 |
| GC (%) | 35.04 |
Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).
| sseqid | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | staxids | stitle |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CP119173 | 99.97 | 10772 | 3 | 0 | 1 | 10772 | 1958 | 12729 | 0 | 19413.6 | nan | Streptococcus macedonicus strain SGM CIP105683 plasmid pSMA198, complete sequence |
| HE613570 | 99.99 | 9582 | 0 | 1 | 1 | 9582 | 3148 | 12728 | 0 | 17273.1 | nan | Streptococcus macedonicus ACA-DC 198 plasmid pSMA198, complete genome |
| OX461091 | 93.62 | 5531 | 329 | 14 | 5297 | 10816 | 2570 | 8087 | 0 | 8342.77 | nan | Streptococcus agalactiae isolate MRI Z2-336 genome assembly, plasmid: IME |
| MW118671 | 93.62 | 5531 | 329 | 14 | 5297 | 10816 | 2570 | 8087 | 0 | 8342.77 | nan | Streptococcus agalactiae strain MRIZ2-336 integrative mobilizable element mobile element, complete sequence |
| CP125109 | 97.58 | 4709 | 81 | 18 | 6121 | 10816 | 1 | 4689 | 0 | 7927.99 | nan | Streptococcus iniae strain GXAS200705 plasmid unnamed1, complete sequence |