Norway rat
NCBI taxon id: | 10116 NCBI; ENA; GoaT |
---|---|
Order: | Rodentia |
Family: | Muridae |
NCBI lineage: | Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Euarchontoglires;Glires;Rodentia;Myomorpha;Muroidea;Muridae;Murinae;Rattus; |
GoaT genome size (M): | 3,198 (direct) |
GoaT asm span (M): | 2,859 (direct) |
GoaT chr no.: | 42 (direct) |
GoaT haploid no.: | 21 (direct) |
GoaT ploidy: | 2 (ancestor) |
ToLID prefix: | mRatNor |
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
tolid | specimen_id | gal | sex | organism_part | biosample | biospecimen |
---|---|---|---|---|---|---|
mRatNor1 | SAN0001274 | SANGER INSTITUTE | MALE | KIDNEY | SAMEA7524437 | SAMEA7524397 |
mRatNor1 | SAN0001274 | SANGER INSTITUTE | MALE | KIDNEY | SAMEA7524437 | SAMEA7524397 |
mRatNor1 | SAN0001274 | SANGER INSTITUTE | MALE | KIDNEY | SAMEA7524437 | SAMEA7524397 |
mRatNor1 | SAN0001274 | SANGER INSTITUTE | MALE | KIDNEY | SAMEA7524437 | SAMEA7524397 |
mRatNor1 | SAN0001274 | SANGER INSTITUTE | MALE | KIDNEY | SAMEA7524437 | SAMEA7524397 |
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.
source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
---|---|---|---|---|---|---|---|---|---|
htag-202110 | mRatNor6 | 31 | 65.24 | 2,867,379,224 | 26.28 | 0.28 | 99.05 | 0.35 | ![]() ![]() histogram.txt |
pacbio | mRatNor10 | 31 | 13.37 | 2,004,767,334 | 27.85 | 1.81 | 98.57 | 0.19 | ![]() ![]() histogram.txt |
pacbio | mRatNor9 | 31 | 17.3 | 2,370,598,866 | 22.24 | 1.14 | 95.25 | 0.13 | ![]() ![]() histogram.txt |
10x | mRatNor1 | 31 | 15.33 | 3,310,516,797 | 37.06 | 0.64 | 98.62 | 0.73 | ![]() ![]() histogram.txt |
hic | mRatNor1 | 31 | 25.17 | 1,841,783,818 | 60.55 | 3.90 | 95.56 | 0.37 | ![]() ![]() histogram.txt |
hic-arima | mRatNor1 | 31 | 36.05 | 2,544,891,374 | 20.73 | 0.40 | 99.15 | 0.44 | ![]() ![]() histogram.txt |
pacbio | mRatNor7 | 31 | 37.89 | 34,135,372 | 89.92 | 3.03 | 85.59 | 5.51 | ![]() ![]() histogram.txt |
pacbio | mRatNor8 | 31 | 15.79 | 2,649,566,472 | 21.90 | 0.39 | 96.97 | 0.13 | ![]() ![]() histogram.txt |
htag-202203 | mRatNor5 | 31 | 37.75 | 2,776,540,286 | 23.68 | 0.28 | 98.61 | 0.33 | ![]() ![]() histogram.txt |
Below are stats for each PacBio seqeuncing run collected for this species.
pipeline | specimen | date | run id | movie | well | tag | yield | N50 | sample accession | run accession | barcode |
---|---|---|---|---|---|---|---|---|---|---|---|
PacBio - CLR | mRatNor1 | 2019-06-18 | 69793 | m64016_190618_103014 | A01 | - | 137,363,443,853 | 39,053 | SAMN16261960 | ||
PacBio - CLR | mRatNor1 | 2019-06-22 | 69905 | m64016_190622_041831 | B01 | - | 127,339,986,206 | 35,554 | SAMN16261960 | ||
PacBio - HiFi | mRatNor7 | 2021-09-09 | 86456 | m64230e_210909_152906 | A01 | 1012 | 5,767,304,402 | 13,858 | |||
PacBio - HiFi | mRatNor7 | 2021-09-10 | 86456 | m64230e_210910_213825 | B01 | 1012 | 9,242,807,942 | 13,846 | |||
PacBio - HiFi | mRatNor8 | 2021-11-15 | 87992 | m64222e_211115_183322 | A01 | - | 28,844,118,522 | 9,930 | |||
PacBio - HiFi | mRatNor9 | 2021-11-17 | 87992 | m64222e_211117_052750 | B01 | - | 28,541,162,119 | 10,050 | |||
PacBio - HiFi | mRatNor10 | 2021-11-18 | 87992 | m64222e_211118_162435 | C01 | - | 26,788,998,990 | 11,133 | |||
PacBio - HiFi | mRatNor10 | 2021-11-18 | 87992 | m64222e_211118_162435 | C01 | - | 29,617,082,180 | 11,150 | |||
PacBio - HiFi | mRatNor8 | 2021-11-25 | 88189 | m64222e_211125_025537 | B01 | - | 29,222,798,276 | 9,798 | |||
PacBio - HiFi | mRatNor9 | 2021-11-26 | 88326 | m64174e_211126_173648 | A01 | - | 28,543,645,061 | 9,912 | |||
PacBio - HiFi | mRatNor8 | 2021-11-26 | 88189 | m64222e_211126_135237 | C01 | - | 29,451,774,240 | 9,839 | |||
PacBio - HiFi | mRatNor10 | 2021-11-28 | 88189 | m64222e_211128_005046 | D01 | - | 27,386,040,209 | 10,991 | |||
PacBio - HiFi | mRatNor10 | 2021-11-28 | 88189 | m64222e_211128_005046 | D01 | - | 24,957,328,321 | 10,967 | |||
PacBio - HiFi | mRatNor9 | 2021-11-28 | 88326 | m64174e_211128_025442 | B01 | - | 28,590,047,405 | 9,893 |
Below are stats for each ONT seqeuncing run collected for this species.
pipeline | specimen | date | run id | flowcell | type | yield | N50 | sample accession | report |
---|---|---|---|---|---|---|---|---|---|
No matching records found |
Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
---|---|---|---|---|---|---|---|---|---|
Haplotagging | mRatNor6 | 2022-03-29 | 41305_1#3 | 553,779,750 | 82,236,292,875 | qc complete | Rattus norvegicus (1.00) | ||
Haplotagging | mRatNor6 | 2022-03-28 | 41302_2#3 | 645,016,616 | 95,784,967,476 | qc complete | |||
Haplotagging | mRatNor6 | 2022-03-29 | 41306#3 | 1,136,919,942 | 168,832,611,387 | qc complete | Rattus norvegicus (1.00) | ||
Haplotagging | mRatNor6 | 2022-03-29 | 41305_2#3 | 580,265,904 | 86,169,486,744 | qc complete | Rattus norvegicus (0.99) | ||
Haplotagging | mRatNor6 | 2022-03-28 | 41302_1#3 | 600,745,674 | 89,210,732,589 | qc complete | |||
Chromium genome | mRatNor1 | 2019-06-12 | 29703_1#3 | 134,746,922 | 20,346,785,222 | SAMN16261960 | qc complete | Rattus norvegicus (1.00) | |
Chromium genome | mRatNor1 | 2019-06-12 | 29703_1#4 | 159,392,818 | 24,068,315,518 | SAMN16261960 | qc complete | Rattus norvegicus (1.00) | |
Chromium genome | mRatNor1 | 2019-06-12 | 29703_2#3 | 139,778,240 | 21,106,514,240 | SAMN16261960 | qc complete | Rattus norvegicus (1.00) | |
Chromium genome | mRatNor1 | 2019-06-12 | 29703_1#1 | 190,271,588 | 28,731,009,788 | SAMN16261960 | qc complete | Rattus norvegicus (1.00) | |
Chromium genome | mRatNor1 | 2019-06-12 | 29703_2#1 | 196,855,598 | 29,725,195,298 | SAMN16261960 | qc complete | Rattus norvegicus (1.00) | |
Chromium genome | mRatNor1 | 2019-06-12 | 29703_1#2 | 134,555,188 | 20,317,833,388 | SAMN16261960 | qc complete | Rattus norvegicus (1.00) | |
Chromium genome | mRatNor1 | 2019-06-12 | 29703_2#2 | 139,178,772 | 21,015,994,572 | SAMN16261960 | qc complete | Rattus norvegicus (1.00) | |
Chromium genome | mRatNor1 | 2019-06-12 | 29703_2#4 | 164,548,402 | 24,846,808,702 | SAMN16261960 | qc complete | Rattus norvegicus (1.00) | |
Hi-C | mRatNor1 | 2019-09-26 | 30821_3#1 | 857,531,968 | 129,487,327,168 | SAMEA7524437 | qc complete | Rattus norvegicus (1.00) | |
Hi-C - Arima v2 | mRatNor1 | 2021-04-13 | 37312#5 | 373,691,676 | 56,427,443,076 | qc complete | Rattus norvegicus (1.00) | ||
Hi-C - Arima v2 | mRatNor1 | 2021-04-13 | 37312#4 | 239,024,922 | 36,092,763,222 | qc complete | Rattus norvegicus (1.00) | ||
Hi-C - Arima v2 | mRatNor1 | 2021-04-13 | 37312#6 | 391,134,270 | 59,061,274,770 | qc complete | Rattus norvegicus (1.00) | ||
Hi-C - Arima v2 | mRatNor1 | 2021-04-13 | 37312#3 | 296,407,326 | 44,757,506,226 | qc complete | |||
Hi-C - Arima v2 | mRatNor1 | 2021-04-13 | 37312#1 | 328,719,880 | 49,636,701,880 | qc complete | Rattus norvegicus (1.00) | ||
Hi-C - Arima v2 | mRatNor1 | 2021-04-13 | 37312#2 | 221,474,942 | 33,442,716,242 | qc complete | Rattus norvegicus (1.00) |
Below are results from a screen of the PacBio data using Mash screen against RefSeq assemblies. Only results with identity over 90% are displayed.
identity | info |
---|---|
0.991166 | [7041 seqs] AC_000069.1 Rattus norvegicus strain BN; Sprague-Dawley chromosome 1, alternate assembly Rn_Celera, whole genome shotgun sequence [...] |
0.910625 | NC_001506.1 Murine osteosarcoma virus, complete genome |
0.907417 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
0.902135 | NC_001499.1 Abelson murine leukemia virus, complete genome |
0.901381 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
0.900394 | NC_021929.1 Malvastrum leaf curl Philippines betasatellite, complete sequence |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
---|---|---|---|
No matching records found |
MarkerScan cobiont assembly by read separation based on observed families (see above). These reads are both aligned to the assembly and independently re-assembled. The quality of these assemblies is assessed by their completeness according to BUSCO, their span and the number of reads they encompass. For more information here.
specimen | family | classified reads | original assembly | re-assembly | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | number of reads | BUSCO | contigs | contig length | number of reads | ||
No matching records found |
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
---|---|
mRatNor1 |
Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.
Features (colours represent quantile bins):
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
---|---|---|---|---|---|---|---|---|---|
No matching records found |
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
---|---|---|---|---|---|---|---|---|---|
No matching records found |