diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 1a1e7fdde..000000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1 +0,0 @@
-include malariagen_data/resources/*
diff --git a/docs/source/Ag3.rst b/docs/source/Ag3.rst
index d4bb77003..c7d4486b0 100644
--- a/docs/source/Ag3.rst
+++ b/docs/source/Ag3.rst
@@ -224,6 +224,7 @@ Inversion karyotypes
     :toctree: generated/
 
     karyotype
+    load_inversion_tags
 
 Phenotype data access
 ---------------------
diff --git a/malariagen_data/adar1.py b/malariagen_data/adar1.py
index 1340a9554..fd0b29180 100644
--- a/malariagen_data/adar1.py
+++ b/malariagen_data/adar1.py
@@ -130,7 +130,6 @@ def __init__(
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
-            inversion_tag_path=None,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,
         )
diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py
index f8c07c61d..be93877af 100644
--- a/malariagen_data/adir1.py
+++ b/malariagen_data/adir1.py
@@ -130,7 +130,6 @@ def __init__(
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
-            inversion_tag_path=None,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,
         )
diff --git a/malariagen_data/af1.py b/malariagen_data/af1.py
index 94d425f2a..c66cd8dee 100644
--- a/malariagen_data/af1.py
+++ b/malariagen_data/af1.py
@@ -132,7 +132,6 @@ def __init__(
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
-            inversion_tag_path=None,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,
         )
diff --git a/malariagen_data/ag3.py b/malariagen_data/ag3.py
index ae425a79f..dec66e30b 100644
--- a/malariagen_data/ag3.py
+++ b/malariagen_data/ag3.py
@@ -27,7 +27,6 @@
 GENE_NAMES = {
     "AGAP004707": "Vgsc/para",
 }
-INVERSION_TAG_PATH = "karyotype_tag_snps.csv"
 
 
 def _setup_aim_palettes():
@@ -213,7 +212,6 @@ def __init__(
             aim_species_colors=AIM_SPECIES_COLORS,
             virtual_contigs=VIRTUAL_CONTIGS,
             gene_names=GENE_NAMES,
-            inversion_tag_path=INVERSION_TAG_PATH,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,
         )
diff --git a/malariagen_data/amin1.py b/malariagen_data/amin1.py
index ae93c6d3a..2923f3465 100644
--- a/malariagen_data/amin1.py
+++ b/malariagen_data/amin1.py
@@ -130,7 +130,6 @@ def __init__(
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
-            inversion_tag_path=None,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,
         )
diff --git a/malariagen_data/anoph/karyotype.py b/malariagen_data/anoph/karyotype.py
index fcfa23f14..b33ea67d8 100644
--- a/malariagen_data/anoph/karyotype.py
+++ b/malariagen_data/anoph/karyotype.py
@@ -36,7 +36,7 @@ def _karyotype_tags_n_alt(gt, alts, inversion_alts):
 class AnophelesKaryotypeAnalysis(AnophelesSnpData):
     def __init__(
         self,
-        inversion_tag_path: Optional[str] = None,
+        karyotype_analysis: Optional[str] = None,
         **kwargs,
     ):
         # N.B., this class is designed to work cooperatively, and
@@ -44,29 +44,51 @@ def __init__(
         # to the superclass constructor.
         super().__init__(**kwargs)
 
-        self._inversion_tag_path = inversion_tag_path
+        # If provided, this analysis version will override the
+        # default value provided in the release configuration.
+        self._karyotype_analysis_override = karyotype_analysis
+
+    @property
+    def _karyotype_analysis(self) -> Optional[str]:
+        if self._karyotype_analysis_override:
+            return self._karyotype_analysis_override
+        else:
+            # N.B., this will return None if the key is not present in the
+            # config.
+            return self.config.get("DEFAULT_KARYOTYPE_ANALYSIS")
+
+    def _require_karyotype_analysis(self):
+        if not self._karyotype_analysis:
+            raise NotImplementedError(
+                "Inversion karyotype analysis is not available for this data resource."
+            )
 
     @_check_types
     @doc(
         summary="Load tag SNPs for a given inversion.",
     )
     def load_inversion_tags(self, inversion: inversion_param) -> pd.DataFrame:
-        # needs to be modified depending on where we are hosting
-        import importlib.resources
-        from .. import resources
+        self._require_karyotype_analysis()
 
-        if self._inversion_tag_path is None:
-            raise NotImplementedError(
-                "No inversion tags are available for this data resource."
+        path = (
+            f"{self._base_path}/{self._major_version_path}"
+            f"/snp_karyotype/{self._karyotype_analysis}/karyotype_tag_snps.csv"
+        )
+        with self._fs.open(path) as f:
+            df_tag_snps = pd.read_csv(f, sep=",")
+
+        # Validate inversion name.
+        available = sorted(df_tag_snps["inversion"].unique())
+        if inversion not in available:
+            raise ValueError(
+                f"Unknown inversion '{inversion}'. Available inversions: {available}"
             )
-        else:
-            with importlib.resources.path(resources, self._inversion_tag_path) as path:
-                df_tag_snps = pd.read_csv(path, sep=",")
-            return df_tag_snps.loc[df_tag_snps["inversion"] == inversion].reset_index()
+
+        return df_tag_snps.query(f"inversion == '{inversion}'").reset_index(drop=True)
 
     @_check_types
     @doc(
-        summary="Infer karyotype from tag SNPs for a given inversion in Ag.",
+        summary="Infer karyotype from tag SNPs for a given inversion.",
     )
     def karyotype(
         self,
@@ -79,7 +101,7 @@ def karyotype(
         df_tagsnps = self.load_inversion_tags(inversion=inversion)
         inversion_pos = df_tagsnps["position"]
         inversion_alts = df_tagsnps["alt_allele"]
-        contig = inversion[0:2]
+        contig = df_tagsnps["contig"].iloc[0]
 
         # get snp calls for inversion region
         start, end = np.min(inversion_pos), np.max(inversion_pos)
diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py
index 8342dbb88..c1bec8658 100644
--- a/malariagen_data/anopheles.py
+++ b/malariagen_data/anopheles.py
@@ -142,7 +142,7 @@ def __init__(
         aim_species_colors: Optional[Mapping[str, str]] = None,
         virtual_contigs: Optional[Mapping[str, Sequence[str]]] = None,
         gene_names: Optional[Mapping[str, str]] = None,
-        inversion_tag_path: Optional[str] = None,
+        karyotype_analysis: Optional[str] = None,
         unrestricted_use_only: Optional[bool] = None,
         surveillance_use_only: Optional[bool] = None,
     ):
@@ -180,7 +180,7 @@ def __init__(
             aim_species_colors=aim_species_colors,
             virtual_contigs=virtual_contigs,
             gene_names=gene_names,
-            inversion_tag_path=inversion_tag_path,
+            karyotype_analysis=karyotype_analysis,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,
         )
diff --git a/malariagen_data/resources/karyotype_tag_snps.csv b/malariagen_data/resources/karyotype_tag_snps.csv
deleted file mode 100644
index b39a264d3..000000000
--- a/malariagen_data/resources/karyotype_tag_snps.csv
+++ /dev/null
@@ -1,1081 +0,0 @@
-inversion,contig,position,alt_allele
-2La,2L,20528221,T
-2La,2L,20542311,A
-2La,2L,20542372,T
-2La,2L,20542904,T
-2La,2L,20546192,A
-2La,2L,20571941,T
-2La,2L,20578023,T
-2La,2L,20581351,A
-2La,2L,20583670,A
-2La,2L,20629290,G
-2La,2L,20630701,T
-2La,2L,20674783,C
-2La,2L,20694485,A
-2La,2L,20698730,T
-2La,2L,20726654,T
-2La,2L,20726658,A
-2La,2L,20729960,G
-2La,2L,20731296,T
-2La,2L,20732483,G
-2La,2L,20742895,A
-2La,2L,20749485,T
-2La,2L,20754096,C
-2La,2L,20754760,T
-2La,2L,20755104,C
-2La,2L,20758474,A
-2La,2L,20762714,G
-2La,2L,20769277,A
-2La,2L,20769367,A
-2La,2L,20769388,C
-2La,2L,20769644,A
-2La,2L,20771498,A
-2La,2L,20813877,T
-2La,2L,20816241,T
-2La,2L,20971238,A
-2La,2L,20982789,C
-2La,2L,20983841,T
-2La,2L,20985959,A
-2La,2L,21014123,G
-2La,2L,21014130,C
-2La,2L,21078564,A
-2La,2L,21078840,C
-2La,2L,21092863,A
-2La,2L,21099293,A
-2La,2L,21099782,T
-2La,2L,21100634,T
-2La,2L,21112810,C
-2La,2L,21119743,T
-2La,2L,21120275,T
-2La,2L,21120654,A
-2La,2L,21127124,A
-2La,2L,21145451,G
-2La,2L,21148755,G
-2La,2L,21148772,T
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-2La,2L,21152623,C
-2La,2L,21303515,G
-2La,2L,21305940,G
-2La,2L,21315321,G
-2La,2L,21327897,A
-2La,2L,21350986,A
-2La,2L,21352486,G
-2La,2L,21359135,C
-2La,2L,21375737,T
-2La,2L,21375838,A
-2La,2L,21375860,C
-2La,2L,21382484,G
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-2Rb,2R,22188409,T
-2Rb,2R,22203733,T
-2Rb,2R,22206425,C
-2Rb,2R,22209028,T
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-2Rb,2R,22257522,A
-2Rb,2R,22261646,A
-2Rb,2R,22276262,A
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-2Rb,2R,22293684,T
-2Rb,2R,22294679,G
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-2Rb,2R,22919684,G
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-2Rb,2R,22942292,C
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-2Rb,2R,22946606,A
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-2Rb,2R,22950446,G
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-2Rb,2R,23168078,T
-2Rb,2R,23168254,T
-2Rb,2R,23168258,A
-2Rb,2R,23170542,T
-2Rb,2R,23170605,G
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-2Rb,2R,23187985,A
-2Rb,2R,23204059,A
-2Rb,2R,23222571,A
-2Rb,2R,23248539,A
-2Rb,2R,23308853,C
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-2Rb,2R,23342730,A
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-2Rb,2R,23427644,T
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-2Rb,2R,23549539,G
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-2Rb,2R,23726725,C
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-2Rb,2R,23997303,T
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-2Rb,2R,24353184,A
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-2Rb,2R,24404091,C
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-2Rb,2R,24574829,A
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-2Rb,2R,24750302,A
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-2Rb,2R,24792625,G
-2Rb,2R,24819958,G
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-2Rb,2R,25033805,G
-2Rb,2R,25052588,G
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-2Rb,2R,25107397,T
-2Rb,2R,25107398,C
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-2Rb,2R,25130459,T
-2Rb,2R,25259589,T
-2Rb,2R,25423714,A
-2Rb,2R,25423784,A
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-2Rb,2R,25456112,A
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-2Rb,2R,25520570,A
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-2Rb,2R,25562481,A
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-2Rb,2R,25708219,C
-2Rb,2R,25718301,C
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-2Rb,2R,25790826,T
-2Rb,2R,25856474,C
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-2Rb,2R,25876512,C
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-2Rb,2R,25890947,T
-2Rb,2R,25897207,G
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-2Rb,2R,25945146,G
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-2Rb,2R,25961467,G
-2Rb,2R,25962183,C
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-2Rb,2R,25964666,G
-2Rb,2R,25964790,A
-2Rb,2R,25965182,A
-2Rb,2R,25967231,T
-2Rb,2R,25982702,G
-2Rb,2R,25984234,A
-2Rb,2R,25984350,T
-2Rb,2R,26008997,G
-2Rb,2R,26178750,C
-2Rb,2R,26193996,G
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-2Rb,2R,26228513,C
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-2Rb,2R,26229905,T
-2Rb,2R,26248614,G
-2Rb,2R,26254834,G
-2Rb,2R,26259109,A
-2Rb,2R,26259123,A
-2Rb,2R,26371581,A
-2Rb,2R,26380901,T
-2Rb,2R,26414602,G
-2Rb,2R,26427790,G
-2Rb,2R,26446866,A
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-2Rb,2R,26472378,T
-2Rb,2R,26658466,T
-2Rb,2R,26660389,G
-2Rb,2R,26694130,C
-2Rb,2R,26743467,A
-2Rb,2R,26746643,C
-2Rb,2R,26746644,A
-2Rb,2R,26746649,T
-2Rb,2R,26746735,C
-2Rb,2R,26746778,C
-2Rd,2R,31523562,T
-2Rd,2R,31610485,C
-2Rd,2R,31614850,G
-2Rd,2R,31614874,T
-2Rd,2R,31615285,T
-2Rd,2R,31616748,A
-2Rd,2R,31629231,G
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-2Rd,2R,31639025,T
-2Rd,2R,31653553,T
-2Rd,2R,31684997,T
-2Rd,2R,32860895,C
-2Rd,2R,32862480,C
-2Rd,2R,32882145,T
-2Rd,2R,33993155,G
-2Rd,2R,35034708,C
-2Rd,2R,35093874,C
-2Rd,2R,35094016,T
-2Rd,2R,35095675,C
-2Rd,2R,35095821,C
-2Rd,2R,35095993,C
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-2Rd,2R,35098106,G
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-2Rd,2R,35098532,T
-2Rd,2R,35098795,T
-2Rd,2R,35102397,G
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-2Rd,2R,35715586,G
-2Rd,2R,35715596,A
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-2Rd,2R,35716630,A
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-2Rd,2R,35718615,C
-2Rd,2R,35718894,C
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-2Rd,2R,35768318,A
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-2Rd,2R,35927871,T
-2Rd,2R,35931331,A
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-2Rd,2R,36195407,C
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-2Rd,2R,36196296,A
-2Rd,2R,36200109,C
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-2Rd,2R,36219896,T
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-2Rd,2R,36220209,A
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-2Rd,2R,36275729,T
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-2Rd,2R,36317242,G
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-2Rd,2R,36462456,A
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-2Rd,2R,36593441,A
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-2Rd,2R,36656217,C
-2Rd,2R,36675489,A
-2Rd,2R,36676536,A
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-2Rd,2R,36682204,G
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-2Rd,2R,36682513,T
-2Rd,2R,36682566,C
-2Rd,2R,36684127,T
-2Rd,2R,36716395,T
-2Rd,2R,36716481,A
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-2Rd,2R,36717266,A
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-2Rd,2R,36717402,T
-2Rd,2R,36717438,C
-2Rd,2R,36717441,A
-2Rd,2R,36718158,G
-2Rd,2R,36718492,A
-2Rd,2R,36719706,A
-2Rd,2R,36720512,T
-2Rd,2R,36721258,A
-2Rd,2R,36916171,G
-2Rd,2R,36926852,T
-2Rd,2R,36926889,T
-2Rd,2R,36928881,T
-2Rd,2R,36928948,T
-2Rd,2R,36948912,T
-2Rd,2R,36957796,T
-2Rd,2R,36993412,A
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-2Rd,2R,37350654,G
-2Rd,2R,37351250,A
-2Rd,2R,37686680,C
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-2Rd,2R,37894422,G
-2Rd,2R,38275741,A
-2Rd,2R,38612980,T
-2Rd,2R,38812337,A
-2Rd,2R,38812537,C
-2Rd,2R,38812664,G
-2Rd,2R,38813556,A
-2Rd,2R,38813559,C
-2Rd,2R,39528753,C
-2Rd,2R,39588534,C
-2Rd,2R,39799497,G
-2Rd,2R,39968896,C
-2Rd,2R,39971868,A
-2Rd,2R,39981770,C
-2Rd,2R,41349565,A
-2Rd,2R,41451632,A
-2Rd,2R,42164430,T
-2Rd,2R,42168396,A
-2Rd,2R,42204119,A
-2Rd,2R,42220746,C
-2Rd,2R,42225360,A
-2Rd,2R,42230996,C
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-2Rd,2R,42253040,A
-2Rd,2R,42278696,T
-2Rd,2R,42289566,T
-2Rd,2R,42299927,A
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-2Rc_gam,2R,28454105,G
-2Rc_gam,2R,28978689,G
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-2Rc_gam,2R,29305153,T
-2Rc_gam,2R,29305276,T
-2Rc_gam,2R,29305383,T
-2Rc_gam,2R,29306134,T
-2Rc_gam,2R,29306197,T
-2Rc_gam,2R,29307769,T
-2Rc_gam,2R,29307919,C
-2Rc_gam,2R,29309864,T
-2Rc_gam,2R,29310166,C
-2Rc_gam,2R,29310191,G
-2Rc_gam,2R,29310201,C
-2Rc_gam,2R,29310253,C
-2Rc_gam,2R,29310296,A
-2Rc_gam,2R,29310336,T
-2Rc_gam,2R,29314785,T
-2Rc_gam,2R,29384371,G
-2Rc_gam,2R,30328642,T
-2Rc_gam,2R,30476017,A
-2Rc_gam,2R,30481345,C
-2Rc_gam,2R,30714057,A
-2Rc_gam,2R,30714060,G
-2Rc_gam,2R,30724210,A
-2Rc_gam,2R,30725625,A
-2Rc_gam,2R,30897767,G
-2Rc_gam,2R,30897771,A
-2Rc_gam,2R,30897774,A
-2Rc_gam,2R,30897775,G
-2Rc_gam,2R,30967698,T
-2Rc_gam,2R,31074641,T
-2Rc_gam,2R,31091052,C
-2Rc_gam,2R,31092050,A
-2Rc_gam,2R,31093974,T
-2Rc_gam,2R,31093987,T
-2Rc_gam,2R,31121606,C
-2Rc_gam,2R,31126113,A
-2Rc_gam,2R,31126453,C
-2Rc_gam,2R,31127706,T
-2Rc_gam,2R,31147129,C
-2Rc_gam,2R,31147132,A
-2Rc_gam,2R,31150175,T
-2Rc_gam,2R,31152120,G
-2Rc_gam,2R,31152351,C
-2Rc_gam,2R,31172511,C
-2Rc_gam,2R,31202061,T
-2Rc_gam,2R,31202064,T
-2Rc_gam,2R,31202076,T
-2Rc_col,2R,27007651,T
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-2Rc_col,2R,27250183,T
-2Rc_col,2R,27254753,A
-2Rc_col,2R,27280531,A
-2Rc_col,2R,27280581,C
-2Rc_col,2R,27280752,T
-2Rc_col,2R,27281084,C
-2Rc_col,2R,27282099,A
-2Rc_col,2R,27282330,T
-2Rc_col,2R,27283425,A
-2Rc_col,2R,27725280,G
-2Rc_col,2R,27740327,T
-2Rc_col,2R,27740592,A
-2Rc_col,2R,28017129,A
-2Rc_col,2R,28017133,A
-2Rc_col,2R,28104728,C
-2Rc_col,2R,28104970,C
-2Rc_col,2R,28113792,G
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-2Rc_col,2R,28122009,C
-2Rc_col,2R,28171113,C
-2Rc_col,2R,28434972,T
-2Rc_col,2R,28468246,A
-2Rc_col,2R,28484341,T
-2Rc_col,2R,28484350,C
-2Rc_col,2R,28776715,T
-2Rc_col,2R,28805094,T
-2Rc_col,2R,28814945,A
-2Rc_col,2R,29026558,C
-2Rc_col,2R,29084286,A
-2Rc_col,2R,29087279,C
-2Rc_col,2R,29134005,G
-2Rc_col,2R,29175698,C
-2Rc_col,2R,29194375,A
-2Rc_col,2R,29268921,A
-2Rc_col,2R,29269103,A
-2Rc_col,2R,29269324,G
-2Rc_col,2R,29269352,C
-2Rc_col,2R,29322912,G
-2Rc_col,2R,29393543,G
-2Rc_col,2R,29393579,G
-2Rc_col,2R,29393593,A
-2Rc_col,2R,29409159,A
-2Rc_col,2R,29415920,G
-2Rc_col,2R,29417833,C
-2Rc_col,2R,29517224,G
-2Rc_col,2R,29517240,C
-2Rc_col,2R,29519609,G
-2Rc_col,2R,29787632,C
-2Rc_col,2R,30355430,G
-2Rc_col,2R,30386671,A
-2Rc_col,2R,30392408,G
-2Rc_col,2R,30523061,T
-2Rc_col,2R,31231129,A
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-2Rc_col,2R,31463934,T
-2Rj,2R,3264090,A
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-2Rj,2R,3264504,A
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-2Rj,2R,3265032,T
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-2Rj,2R,3267404,C
-2Rj,2R,3267929,G
-2Rj,2R,3268001,A
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-2Rj,2R,3269237,A
-2Rj,2R,3270801,A
-2Rj,2R,3274227,T
-2Rj,2R,3274229,G
-2Rj,2R,3274806,C
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-2Rj,2R,3276108,A
-2Rj,2R,3276813,C
-2Rj,2R,3277024,T
-2Rj,2R,3277356,A
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-2Rj,2R,3278288,A
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-2Rj,2R,3281412,A
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-2Rj,2R,3288528,T
-2Rj,2R,3288561,C
-2Rj,2R,3299675,A
-2Rj,2R,3300002,T
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-2Rj,2R,3301197,A
-2Rj,2R,3301739,A
-2Rj,2R,3302459,A
-2Rj,2R,3302603,A
-2Rj,2R,3302698,G
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-2Rj,2R,3303715,T
-2Rj,2R,3304231,T
-2Rj,2R,3304469,C
-2Rj,2R,3306289,C
-2Rj,2R,3306290,A
-2Rj,2R,3307638,A
-2Rj,2R,3308920,T
-2Rj,2R,3325788,A
-2Rj,2R,3341654,C
-2Rj,2R,10916292,C
-2Rj,2R,11234277,T
-2Rj,2R,11234287,C
-2Rj,2R,11234497,C
-2Rj,2R,13585215,T
-2Rj,2R,13598254,A
-2Rj,2R,15555216,A
-2Rj,2R,15556093,G
-2Rj,2R,15705549,T
-2Rj,2R,15706857,T
-2Rj,2R,15708973,T
-2Rj,2R,15710203,T
-2Rj,2R,15711499,T
-2Rj,2R,15711596,T
-2Rj,2R,15712475,T
-2Rj,2R,15712693,A
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-2Rj,2R,15713100,A
-2Rj,2R,15714321,A
-2Rj,2R,15716132,T
-2Rj,2R,15716428,G
-2Rj,2R,15718542,T
-2Rj,2R,15719084,A
-2Rj,2R,15720433,T
-2Rj,2R,15732334,C
-2Rj,2R,15732338,T
-2Rj,2R,15740463,T
-2Rj,2R,15740657,A
-2Rj,2R,15740931,C
-2Rj,2R,15740978,T
-2Rj,2R,15741314,G
-2Rj,2R,15742834,T
-2Rj,2R,15743161,A
-2Rj,2R,15743203,A
-2Rj,2R,15743636,G
-2Rj,2R,15745595,A
-2Rj,2R,15746439,A
-2Rj,2R,15747295,G
-2Rj,2R,15747386,C
-2Rj,2R,15747519,G
-2Rj,2R,15747695,T
-2Rj,2R,15748347,G
-2Rj,2R,15748971,A
-2Rj,2R,15749248,A
-2Rj,2R,15749285,T
-2Rj,2R,15750449,T
-2Ru,2R,31516240,T
-2Ru,2R,31516340,C
-2Ru,2R,31516795,C
-2Ru,2R,31517127,A
-2Ru,2R,31517528,T
-2Ru,2R,31517733,G
-2Ru,2R,31517858,G
-2Ru,2R,31518159,C
-2Ru,2R,31518839,A
-2Ru,2R,31523460,G
-2Ru,2R,31553046,A
-2Ru,2R,31557927,C
-2Ru,2R,31558044,T
-2Ru,2R,31558111,T
-2Ru,2R,31558469,T
-2Ru,2R,31560220,A
-2Ru,2R,31560735,T
-2Ru,2R,31563611,C
-2Ru,2R,31567669,T
-2Ru,2R,31568447,T
-2Ru,2R,31694267,A
-2Ru,2R,31703855,G
-2Ru,2R,31705832,G
-2Ru,2R,31706650,T
-2Ru,2R,31710083,C
-2Ru,2R,31710302,C
-2Ru,2R,31710303,T
-2Ru,2R,31710305,A
-2Ru,2R,31710369,G
-2Ru,2R,31710915,T
-2Ru,2R,31711195,C
-2Ru,2R,31713353,T
-2Ru,2R,31715733,T
-2Ru,2R,31719403,T
-2Ru,2R,31756006,T
-2Ru,2R,31757751,T
-2Ru,2R,31761812,T
-2Ru,2R,31761967,G
-2Ru,2R,31762081,T
-2Ru,2R,31881417,A
-2Ru,2R,31903706,G
-2Ru,2R,31914348,A
-2Ru,2R,31936521,C
-2Ru,2R,31936715,T
-2Ru,2R,31937094,A
-2Ru,2R,31941065,A
-2Ru,2R,31942143,C
-2Ru,2R,32021333,G
-2Ru,2R,32021855,A
-2Ru,2R,32022565,A
-2Ru,2R,32022571,C
-2Ru,2R,32023835,C
-2Ru,2R,32024114,T
-2Ru,2R,32035375,T
-2Ru,2R,32036381,G
-2Ru,2R,32069754,G
-2Ru,2R,32069796,C
-2Ru,2R,32085587,G
-2Ru,2R,32186487,G
-2Ru,2R,32186515,C
-2Ru,2R,32187926,A
-2Ru,2R,32259877,A
-2Ru,2R,32334045,A
-2Ru,2R,32345688,T
-2Ru,2R,32389180,T
-2Ru,2R,32389955,T
-2Ru,2R,32391064,A
-2Ru,2R,32391115,A
-2Ru,2R,32454642,A
-2Ru,2R,32455088,C
-2Ru,2R,32455416,C
-2Ru,2R,32455477,A
-2Ru,2R,32456078,C
-2Ru,2R,32456084,C
-2Ru,2R,32456100,G
-2Ru,2R,32457600,A
-2Ru,2R,32578054,G
-2Ru,2R,32667533,T
-2Ru,2R,32683852,T
-2Ru,2R,32783950,T
-2Ru,2R,32837417,G
-2Ru,2R,32864046,A
-2Ru,2R,32867333,C
-2Ru,2R,32868032,A
-2Ru,2R,32874840,G
-2Ru,2R,32875403,T
-2Ru,2R,32875417,A
-2Ru,2R,32969453,A
-2Ru,2R,32970067,T
-2Ru,2R,32970693,C
-2Ru,2R,32970938,C
-2Ru,2R,32992157,G
-2Ru,2R,33219359,T
-2Ru,2R,33244517,C
-2Ru,2R,33263900,C
-2Ru,2R,33265687,A
-2Ru,2R,33265726,G
-2Ru,2R,33266311,G
-2Ru,2R,33318408,C
-2Ru,2R,33322045,C
-2Ru,2R,33340915,A
-2Ru,2R,33430169,T
-2Ru,2R,33430227,A
-2Ru,2R,33432734,T
-2Ru,2R,33432741,C
-2Ru,2R,33530545,A
-2Ru,2R,33530587,A
-2Ru,2R,33531272,A
-2Ru,2R,33531440,C
-2Ru,2R,33531465,C
-2Ru,2R,33531510,G
-2Ru,2R,33531524,A
-2Ru,2R,33605881,G
-2Ru,2R,33613826,A
-2Ru,2R,33640613,A
-2Ru,2R,33697365,C
-2Ru,2R,33776367,A
-2Ru,2R,33834025,A
-2Ru,2R,34072431,A
-2Ru,2R,34123399,C
-2Ru,2R,34123484,T
-2Ru,2R,34124219,T
-2Ru,2R,34124287,T
-2Ru,2R,34125748,A
-2Ru,2R,34128662,T
-2Ru,2R,34132663,A
-2Ru,2R,34138577,T
-2Ru,2R,34138591,T
-2Ru,2R,34142017,A
-2Ru,2R,34147633,T
-2Ru,2R,34175319,T
-2Ru,2R,34332338,A
-2Ru,2R,34343157,C
-2Ru,2R,34343989,T
-2Ru,2R,34347394,T
-2Ru,2R,34350693,T
-2Ru,2R,34352080,G
-2Ru,2R,34358302,T
-2Ru,2R,34397401,C
-2Ru,2R,34420116,A
-2Ru,2R,34420126,A
-2Ru,2R,34422482,C
-2Ru,2R,34424106,C
-2Ru,2R,34429402,G
-2Ru,2R,34432021,A
-2Ru,2R,34432086,C
-2Ru,2R,34433444,A
-2Ru,2R,34434289,A
-2Ru,2R,34451733,T
-2Ru,2R,34697268,T
-2Ru,2R,34702912,T
-2Ru,2R,34702931,T
-2Ru,2R,34739085,A
-2Ru,2R,34739416,C
-2Ru,2R,34739767,G
-2Ru,2R,34740162,T
-2Ru,2R,34740307,A
-2Ru,2R,34741288,A
-2Ru,2R,34870982,T
-2Ru,2R,34888110,A
-2Ru,2R,34907054,A
-2Ru,2R,35236293,A
-2Ru,2R,35271668,G
-2Ru,2R,35297836,A
-2Ru,2R,35305761,G
-2Ru,2R,35355667,C
-2Ru,2R,35355964,G
-2Ru,2R,35373216,C
-2Ru,2R,35373702,T
-2Ru,2R,35373966,T
-2Ru,2R,35404397,C
-2Ru,2R,35408302,T
-2Ru,2R,35488437,G
-2Ru,2R,35488795,A
-2Ru,2R,35489077,G
-2Ru,2R,35496370,A
-2Ru,2R,35498331,G
diff --git a/tests/anoph/conftest.py b/tests/anoph/conftest.py
index f94768ad3..165c2755c 100644
--- a/tests/anoph/conftest.py
+++ b/tests/anoph/conftest.py
@@ -1030,6 +1030,7 @@ def __init__(
         self.init_genome_features()
         self.init_metadata()
         self.init_snp_sites()
+        self.init_karyotype_tags()
         self.init_site_filters()
         self.init_snp_genotypes()
         self.init_site_annotations()
@@ -1094,6 +1095,9 @@ def init_metadata(self):
     def init_snp_sites(self):
         pass
 
+    def init_karyotype_tags(self):
+        pass
+
     def init_site_filters(self):
         pass
 
@@ -1150,6 +1154,7 @@ def init_config(self):
             "SITE_ANNOTATIONS_ZARR_PATH": "reference/genome/agamp4/Anopheles-gambiae-PEST_SEQANNOTATION_AgamP4.12.zarr",
             "DEFAULT_AIM_ANALYSIS": "20220528",
             "DEFAULT_SITE_FILTERS_ANALYSIS": "dt_20200416",
+            "DEFAULT_KARYOTYPE_ANALYSIS": "simtest",
             "DEFAULT_COHORTS_ANALYSIS": "20230516",
             "SITE_MASK_IDS": ["gamb_colu_arab", "gamb_colu", "arab"],
             "PHASING_ANALYSIS_IDS": ["gamb_colu_arab", "gamb_colu", "arab"],
@@ -1519,6 +1524,40 @@ def init_snp_sites(self):
             path=path, contigs=self.contigs, genome=self.genome
         )
 
+    def init_karyotype_tags(self):
+        analysis = self.config["DEFAULT_KARYOTYPE_ANALYSIS"]
+
+        # Generate tag SNP data using positions from simulated SNP sites.
+        # N.B., inversions are defined here with their contigs explicitly
+        # rather than derived via string slicing, for robustness.
+        tags = []
+        for contig, inversion in [("2L", "2La"), ("2R", "2Rb")]:
+            snp_pos = self.snp_sites[contig]["variants"]["POS"][:]
+            snp_alt = self.snp_sites[contig]["variants"]["ALT"][:]
+            n_tags = min(20, len(snp_pos))
+            indices = self.rng.choice(len(snp_pos), size=n_tags, replace=False)
+            indices.sort()
+            for idx in indices:
+                tags.append(
+                    {
+                        "inversion": inversion,
+                        "contig": contig,
+                        "position": int(snp_pos[idx]),
+                        "alt_allele": snp_alt[idx][0].decode(),
+                    }
+                )
+
+        df = pd.DataFrame(tags)
+        path = (
+            self.bucket_path
+            / "v3"
+            / "snp_karyotype"
+            / analysis
+            / "karyotype_tag_snps.csv"
+        )
+        path.parent.mkdir(parents=True, exist_ok=True)
+        df.to_csv(path, index=False)
+
     def init_site_filters(self):
         analysis = self.config["DEFAULT_SITE_FILTERS_ANALYSIS"]
 
diff --git a/tests/anoph/test_karyotype.py b/tests/anoph/test_karyotype.py
new file mode 100644
index 000000000..a3b9e44a9
--- /dev/null
+++ b/tests/anoph/test_karyotype.py
@@ -0,0 +1,89 @@
+import pandas as pd
+import pytest
+
+from malariagen_data import ag3 as _ag3
+from malariagen_data import af1 as _af1
+from malariagen_data.anoph.karyotype import AnophelesKaryotypeAnalysis
+
+
+@pytest.fixture
+def ag3_sim_api(ag3_sim_fixture):
+    return AnophelesKaryotypeAnalysis(
+        url=ag3_sim_fixture.url,
+        public_url=ag3_sim_fixture.url,
+        config_path=_ag3.CONFIG_PATH,
+        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
+        major_version_path=_ag3.MAJOR_VERSION_PATH,
+        pre=True,
+        gff_gene_type="gene",
+        gff_gene_name_attribute="Name",
+        gff_default_attributes=("ID", "Parent", "Name", "description"),
+    )
+
+
+@pytest.fixture
+def af1_sim_api(af1_sim_fixture):
+    return AnophelesKaryotypeAnalysis(
+        url=af1_sim_fixture.url,
+        public_url=af1_sim_fixture.url,
+        config_path=_af1.CONFIG_PATH,
+        major_version_number=_af1.MAJOR_VERSION_NUMBER,
+        major_version_path=_af1.MAJOR_VERSION_PATH,
+        pre=True,
+        gff_gene_type="protein_coding_gene",
+        gff_gene_name_attribute="Note",
+        gff_default_attributes=("ID", "Parent", "Note", "description"),
+    )
+
+
+def test_load_inversion_tags(ag3_sim_api):
+    df = ag3_sim_api.load_inversion_tags(inversion="2Rb")
+    assert isinstance(df, pd.DataFrame)
+    assert set(df.columns) >= {"inversion", "contig", "position", "alt_allele"}
+    assert (df["inversion"] == "2Rb").all()
+    assert (df["contig"] == "2R").all()
+    assert len(df) > 0
+
+
+def test_load_inversion_tags_2la(ag3_sim_api):
+    df = ag3_sim_api.load_inversion_tags(inversion="2La")
+    assert isinstance(df, pd.DataFrame)
+    assert (df["inversion"] == "2La").all()
+    assert (df["contig"] == "2L").all()
+    assert len(df) > 0
+
+
+def test_load_inversion_tags_invalid(ag3_sim_api):
+    with pytest.raises(ValueError, match="Unknown inversion"):
+        ag3_sim_api.load_inversion_tags(inversion="X_x")
+
+
+def test_load_inversion_tags_not_implemented(af1_sim_api):
+    with pytest.raises(NotImplementedError):
+        af1_sim_api.load_inversion_tags(inversion="2La")
+
+
+def test_karyotype(ag3_sim_api):
+    df = ag3_sim_api.karyotype(inversion="2Rb")
+    assert isinstance(df, pd.DataFrame)
+    expected_cols = {
+        "sample_id",
+        "inversion",
+        "karyotype_2Rb_mean",
+        "karyotype_2Rb",
+        "total_tag_snps",
+    }
+    assert set(df.columns) == expected_cols
+    assert (df["inversion"] == "2Rb").all()
+    assert all(df["karyotype_2Rb"].isin([0, 1, 2]))
+    assert all(df["karyotype_2Rb_mean"].between(0, 2))
+
+
+def test_karyotype_invalid_inversion(ag3_sim_api):
+    with pytest.raises(ValueError, match="Unknown inversion"):
+        ag3_sim_api.karyotype(inversion="X_x")
+
+
+def test_karyotype_not_implemented(af1_sim_api):
+    with pytest.raises(NotImplementedError):
+        af1_sim_api.karyotype(inversion="2La")