191 markers from Du et al 2023 #137
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standage
commented
Aug 22, 2023
| @@ -1077,6 +1086,7 @@ Marker mh12WL-003 as defined in Yu2022G2 was defined previously and is redundant | |||
| Marker mh12WL-003 as defined in Yu2022G3 was defined previously and is redundant | |||
| Marker mh12WL-003 as defined in Yu2022G4 was defined previously and is redundant | |||
| Marker mh12WL-004 as defined in Yu2022G2 was defined previously and is redundant | |||
| Marker mh12WL-048 as defined in Du2023 was defined previously and is redundant | |||
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I've confirmed the authors' claim that only a single MH published in this study is an exact duplicate of a previously published MH.
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| [Du2023] mh12SHY-001 --> mh12SHY-001.v4 | ||
| [Du2023] mh02WL-002 --> mh02WL-002.v4 | ||
| [Du2023] mh04WL-023 --> mh04WL-023.v5 | ||
| [Du2023] mh11WL-005 --> mh11WL-005.v3 | ||
| [Du2023] mh12WL-048 --> mh12WL-048.v1 | ||
| [Du2023] mh18SCUZJ-0052717 --> mh18SCUZJ-0052717.v2 | ||
| [Du2023] mh07ZHA-004 --> mh07ZHA-004.v2 | ||
| [Du2023] mh01WL-077 --> mh01WL-077.v2 | ||
| [Du2023] mh04WL-074 --> mh04WL-074.v2 |
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Less than 10 had any overlap whatsoever with previously published markers.
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| panel = microhapdb.markers[ | ||
| microhapdb.markers.Source.str.contains("Pakstis2021") | ||
| & microhapdb.markers.Name.str.startswith(loci) | ||
| ] | ||
| return sorted(panel.Name) |
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Bugfix. Rather than explicitly specifying the precise marker identifier, updated this function to use the locus identifier and cross-reference with the Pakstis 2021 paper to grab the appropriate marker identifier.
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This PR adds 191 markers from Du et al 2023. The markers range from 50-200 bp in length, and unfortunately seem to be relatively unimpressive in terms of allelic variation. Only two markers have a global average$A_e \gt 5.0$ , and both of these are alternative definitions for microhaps previously published by others: mh02LS-2qE spans the same 201 bp as mh02WL-002, but its 4 SNPs have an $A_e = 9.258$ versus the 5 SNPs from mh02WL-002.v2 (Yu 2022 Group 3) with an $A_e = 10.233$ ; likewise, mh18LS-18pB includes 3 SNPs spanning 110 bp with an $A_e = 5.35$ , versus the overlapping mh18SCUZJ-0052717.v1 (Zhu2023) which includes 6 SNPs spanning 347 bp with an $A_e = 11.444$ .
Closes #122.