The norSTR package contains a genetic map of 51 autosomal STR markers and allele frequency databases for several populations. The marker panel includes the CODIS core loci and markers from commercial kits such as Fusion 6C and SureID27.
Details and references for the physical positions are provided in data-raw/STR51_GRCh38_positions.xlsx
Genetic positions were obtained from these coordinates using
ibdsim2::convertPos(), based on the recombination map of
Halldorsson et al. (2019). Allele frequency databases were compiled from
published sources and in-house data.
These databases are maintained and used for kinship analysis by the Department of Forensic Sciences in Oslo, Norway. The norSTR package is used by KLINK and other packages in the pedsuite ecosystem.
A minimum allele frequency of 0.001 was applied in all databases. Frequencies below this threshold were adjusted to 0.001.
The current map contains physical and genetic positions of 51 markers:
norSTR::map51
#> Marker Chr Mb cM Kit
#> 1 D1S1656 1 230.769650 230.7204652 Fusion6C/SureID
#> 2 TPOX 2 1.489669 1.1163250 Fusion6C
#> 3 D2S1360 2 17.310841 36.2409800 HDplex
#> 4 D2S441 2 68.011971 87.1020434 Fusion6C/SureID
#> 5 D2S1338 2 218.014905 209.8960998 Fusion6C
#> 6 D3S1358 3 45.540771 66.1807780 Fusion6C
#> 7 D3S3045 3 107.271162 115.0798282 SureID27
#> 8 D3S1744 3 147.374887 151.4572629 HDplex/SureID
#> 9 D4S2366 4 6.483085 13.6176160 HDplex/SureID
#> 10 FGA 4 154.587780 149.5041162 Fusion6C
#> 11 D5S2500 5 59.401368 69.5750700 HDplex
#> 12 D5S2800 5 59.403166 69.5761683 SureID
#> 13 D5S818 5 123.775577 122.2931903 Fusion6C
#> 14 CSF1PO 5 150.076349 148.4949187 Fusion6C
#> 15 D6S477 6 6.140339 15.7286668 SureID27
#> 16 SE33 6 88.277194 91.1317155 Fusion6C
#> 17 D6S1043 6 91.740249 95.9522068 VeriFiler Plus
#> 18 D6S474 6 112.557985 114.5769915 HDplex/SureID
#> 19 D7S3048 7 21.227159 33.1966307 SureID
#> 20 D7S820 7 84.160252 93.0701531 Fusion6C
#> 21 D7S1517 7 123.857797 122.4788499 HDplex
#> 22 D8S1132 8 106.316718 109.2316752 HDplex/SureID
#> 23 D8S1179 8 124.894891 125.5366979 Fusion6C
#> 24 D9S1122 9 77.073849 72.3841905 SureID
#> 25 D10S1435 10 2.201192 3.4694743 SureID27
#> 26 D10S2325 10 12.751096 29.5915101 HDplex
#> 27 D10S1248 10 129.294270 159.4941857 Fusion6C/SureID
#> 28 TH01 11 2.171101 2.9186720 Fusion6C
#> 29 D11S2368 11 19.259634 31.4332432 SureID
#> 30 D11S554 11 44.908802 61.8057270 Phoenix
#> 31 APOC3 11 116.831266 118.1477198 Phoenix
#> 32 vWA 12 5.984011 15.1782196 Fusion6C
#> 33 D12S391 12 12.297057 26.5966621 Fusion6C/SureID
#> 34 D13S325 13 42.599274 43.3800572 SureID
#> 35 D13S317 13 82.148047 77.0896872 Fusion6C
#> 36 D14S1434 14 94.842079 93.0163469 SureID
#> 37 D15S659 15 46.081858 36.2320889 SureID
#> 38 Penta E 15 96.831027 104.1418134 Fusion6C
#> 39 D16S539 16 86.352723 119.1761547 Fusion6C/SureID
#> 40 D17S906 17 6.793179 17.8955494 Phoenix
#> 41 D17S1301 17 74.684878 108.9365840 SureID
#> 42 D18S51 18 63.281703 84.0104672 Fusion6C
#> 43 D18S1364 18 65.732968 87.5228364 SureID
#> 44 D19S253 19 15.617439 37.6922845 SureID
#> 45 D19S433 19 29.926267 49.6952510 Fusion6C
#> 46 D20S482 20 4.525720 11.6574767 SureID
#> 47 D21S11 21 19.182036 11.9370663 Fusion6C
#> 48 D21S2055 21 39.819589 45.2859004 HDplex/SureID
#> 49 Penta D 21 43.636237 57.6024347 Fusion6C
#> 50 D22GATA198B05 22 17.169846 0.4022963 SureID
#> 51 D22S1045 22 37.140312 41.2973845 Fusion6C/SureIDFor convenience, the package provides subsets of markers corresponding to widely-used kits and panels:
norSTR::markerSets
#> $codis
#> [1] "D1S1656" "TPOX" "D2S441" "D2S1338" "D3S1358" "FGA"
#> [7] "D5S818" "CSF1PO" "SE33" "D7S820" "D8S1179" "D10S1248"
#> [13] "TH01" "vWA" "D12S391" "D13S317" "D16S539" "D18S51"
#> [19] "D19S433" "D21S11" "D22S1045"
#>
#> $fusion6c
#> [1] "D1S1656" "TPOX" "D2S441" "D2S1338" "D3S1358" "FGA"
#> [7] "D5S818" "CSF1PO" "SE33" "D7S820" "D8S1179" "D10S1248"
#> [13] "TH01" "vWA" "D12S391" "D13S317" "Penta E" "D16S539"
#> [19] "D18S51" "D19S433" "D21S11" "Penta D" "D22S1045"
#>
#> $globalfiler
#> [1] "D1S1656" "TPOX" "D2S441" "D2S1338" "D3S1358" "FGA"
#> [7] "D5S818" "CSF1PO" "SE33" "D7S820" "D8S1179" "D10S1248"
#> [13] "TH01" "vWA" "D12S391" "D13S317" "D16S539" "D18S51"
#> [19] "D19S433" "D21S11" "D22S1045"
#>
#> $hdplex
#> [1] "D2S1360" "D3S1744" "D4S2366" "D5S2500" "D6S474" "D7S1517" "D8S1132"
#> [8] "D10S2325" "D21S2055"
#>
#> $phoenix
#> [1] "D11S554" "APOC3" "D17S906"
#>
#> $sureid
#> [1] "D1S1656" "D2S441" "D3S1744" "D4S2366"
#> [5] "D5S2800" "D6S474" "D7S3048" "D8S1132"
#> [9] "D9S1122" "D10S1248" "D11S2368" "D12S391"
#> [13] "D13S325" "D14S1434" "D15S659" "D16S539"
#> [17] "D17S1301" "D18S1364" "D19S253" "D20S482"
#> [21] "D21S2055" "D22GATA198B05" "D22S1045"
#>
#> $sureid27
#> [1] "D1S1656" "D2S441" "D3S1744" "D3S3045"
#> [5] "D4S2366" "D5S2800" "D6S474" "D6S477"
#> [9] "D7S3048" "D8S1132" "D9S1122" "D10S1248"
#> [13] "D10S1435" "D11S2368" "D12S391" "D13S325"
#> [17] "D14S1434" "D15S659" "D16S539" "D17S1301"
#> [21] "D18S1364" "D19S253" "D20S482" "D21S2055"
#> [25] "D22GATA198B05" "D22S1045"The package can be installed from CRAN with the following command:
install.packages("norSTR")