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Prepare for public release on Gitea: simurgarray package names, community files, Gitea templates, pseudonymised P6 probe names
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kemal committed 2026-09-30 12:09:13 +01:00
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docs/validation/P6_gsa36_vs_gtctovcf.json
+110 -109
View File
@@ -6,26 +6,26 @@
"probes_in_merged_records": 37785,
"probes_only_in_oracle": 22400,
"only_in_oracle_examples": [
"10:135332149_CNV_CYP2E1",
"10:135332539_CNV_CYP2E1",
"10:135332749_CNV_CYP2E1",
"10:135333169_CNV_CYP2E1",
"10:135333379_CNV_CYP2E1",
"10:135333589_CNV_CYP2E1",
"10:135333799_CNV_CYP2E1",
"10:135334009_CNV_CYP2E1",
"10:135334009_CNV_CYP2E1_ilmndup1",
"10:135334219_CNV_CYP2E1",
"10:135334429_CNV_CYP2E1",
"10:135334639_CNV_CYP2E1",
"10:135334849_CNV_CYP2E1",
"10:135335059_CNV_CYP2E1",
"10:135335569_CNV_CYP2E1",
"10:135335569_CNV_CYP2E1_ilmndup1",
"10:135335869_CNV_CYP2E1",
"10:135335869_CNV_CYP2E1_ilmndup1",
"10:135336079_CNV_CYP2E1",
"10:135336289_CNV_CYP2E1"
"locus_0001",
"locus_0002",
"locus_0003",
"locus_0004",
"locus_0005",
"locus_0006",
"locus_0007",
"locus_0008",
"locus_0009",
"locus_0010",
"locus_0011",
"locus_0012",
"locus_0013",
"locus_0014",
"locus_0015",
"locus_0016",
"locus_0017",
"locus_0018",
"locus_0019",
"locus_0020"
],
"categories": {
"grouping_differs": 155,
@@ -42,7 +42,7 @@
"oracle_site_includes_probes_we_skip": [
[
"207895980019_R03C01",
"ilmnseq_rs529038948_ilmnrev",
"locus_0085",
[
"1",
"201085496",
@@ -60,7 +60,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs529038948_ilmnrev_F2BT",
"locus_0086",
[
"1",
"201085496",
@@ -78,7 +78,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs578144976",
"locus_0087",
[
"10",
"94981305",
@@ -96,7 +96,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs578144976_ilmnfwd_F2BT",
"locus_0088",
[
"10",
"94981305",
@@ -114,7 +114,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs578144976_ilmnrev_F2BT",
"locus_0089",
[
"10",
"94981305",
@@ -132,7 +132,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs2860977_ilmnfwd_F2BT",
"locus_0090",
[
"10",
"95063364",
@@ -150,7 +150,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs11045893_ilmnfwd",
"locus_0091",
[
"12",
"21239885",
@@ -168,7 +168,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_16:55856356",
"locus_0092",
[
"16",
"55822444",
@@ -186,7 +186,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs9947507_ilmnfwd",
"locus_0093",
[
"18",
"657095",
@@ -204,7 +204,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs77654350_ilmnfwd",
"locus_0094",
[
"18",
"664286",
@@ -222,7 +222,7 @@
],
[
"207895980019_R03C01",
"rs150569967",
"locus_0095",
[
"19",
"39244961",
@@ -240,7 +240,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs28416813_ilmnfwd_F2BT",
"locus_0096",
[
"19",
"39245004",
@@ -258,7 +258,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs28416813_ilmnfwd_F2BT_ilmndup1",
"locus_0097",
[
"19",
"39245004",
@@ -276,7 +276,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs28416813_ilmnfwd_F2BT_ilmndup2",
"locus_0098",
[
"19",
"39245004",
@@ -294,7 +294,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs28416813_ilmnrev_F2BT",
"locus_0099",
[
"19",
"39245004",
@@ -312,7 +312,7 @@
],
[
"207895980019_R03C01",
"19:41351926",
"locus_0100",
[
"19",
"40846021",
@@ -330,7 +330,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs114114578_ilmnrev",
"locus_0101",
[
"19",
"40849103",
@@ -348,7 +348,7 @@
],
[
"207895980019_R03C01",
"rs121909682",
"locus_0102",
[
"2",
"85552428",
@@ -366,7 +366,7 @@
],
[
"207895980019_R03C01",
"seq-rs796053097",
"locus_0103",
[
"2",
"166073440",
@@ -384,7 +384,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs574780348_ilmnfwd",
"locus_0104",
[
"22",
"42126481",
@@ -404,7 +404,7 @@
"grouping_differs": [
[
"207895980019_R03C01",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -422,7 +422,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs11280056",
"locus_0106",
[
"18",
"673443",
@@ -440,7 +440,7 @@
],
[
"207895980019_R03C01",
"rs16430",
"locus_0107",
[
"18",
"673443",
@@ -458,7 +458,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -476,7 +476,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs11280056",
"locus_0106",
[
"18",
"673443",
@@ -494,7 +494,7 @@
],
[
"207895980019_R03C02",
"rs16430",
"locus_0107",
[
"18",
"673443",
@@ -512,7 +512,7 @@
],
[
"207895980019_R04C01",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -530,7 +530,7 @@
],
[
"207895980019_R04C01",
"ilmnseq_rs11280056",
"locus_0106",
[
"18",
"673443",
@@ -548,7 +548,7 @@
],
[
"207895980019_R04C01",
"rs16430",
"locus_0107",
[
"18",
"673443",
@@ -566,7 +566,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -584,7 +584,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs11280056",
"locus_0106",
[
"18",
"673443",
@@ -602,7 +602,7 @@
],
[
"207895980019_R05C01",
"rs16430",
"locus_0107",
[
"18",
"673443",
@@ -620,7 +620,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs333_ilmnfwd",
"locus_0108",
[
"3",
"46373452",
@@ -638,7 +638,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs333_ilmnfwd_F2BTindel",
"locus_0109",
[
"3",
"46373452",
@@ -656,7 +656,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs333_ilmnrev",
"locus_0110",
[
"3",
"46373452",
@@ -674,7 +674,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs333_ilmnrev_F2BTindel",
"locus_0111",
[
"3",
"46373452",
@@ -692,7 +692,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs35854239_ilmnfwd",
"locus_0112",
[
"6",
"160139865",
@@ -710,7 +710,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs36056065",
"locus_0113",
[
"6",
"160139865",
@@ -728,7 +728,7 @@
],
[
"207895980019_R06C01",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -746,7 +746,7 @@
],
[
"207895980019_R06C01",
"ilmnseq_rs333_ilmnfwd",
"locus_0108",
[
"3",
"46373452",
@@ -766,7 +766,7 @@
"oracle_opposite_strand_indel_bug": [
[
"207895980019_R03C01",
"ilmnseq_rs3834939",
"locus_0114",
[
"12",
"21334835",
@@ -784,7 +784,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs3834939_ilmnfwd_F2BTindel",
"locus_0115",
[
"12",
"21334835",
@@ -802,7 +802,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs3834939_ilmnrev",
"locus_0116",
[
"12",
"21334835",
@@ -820,7 +820,7 @@
],
[
"207895980019_R03C01",
"rs3834939",
"locus_0117",
[
"12",
"21334835",
@@ -838,7 +838,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs540086241_ilmnfwd_F2BTindel",
"locus_0118",
[
"6",
"33087504",
@@ -856,7 +856,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs540086241_ilmnrev_deg3a2b0",
"locus_0119",
[
"6",
"33087504",
@@ -874,7 +874,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs59782580_ilmnrev_deg3a1b0",
"locus_0120",
[
"7",
"140836521",
@@ -892,7 +892,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs59782580_ilmnrev_F2BTindel",
"locus_0121",
[
"7",
"140836521",
@@ -910,7 +910,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs59782580_ilmnrev_F2BTindel_deg3a1b1",
"locus_0122",
[
"7",
"140836521",
@@ -928,7 +928,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs3834939",
"locus_0114",
[
"12",
"21334835",
@@ -946,7 +946,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs3834939_ilmnfwd_F2BTindel",
"locus_0115",
[
"12",
"21334835",
@@ -964,7 +964,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs3834939_ilmnrev",
"locus_0116",
[
"12",
"21334835",
@@ -982,7 +982,7 @@
],
[
"207895980019_R03C02",
"rs3834939",
"locus_0117",
[
"12",
"21334835",
@@ -1000,7 +1000,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs540086241_ilmnfwd_F2BTindel",
"locus_0118",
[
"6",
"33087504",
@@ -1018,7 +1018,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs540086241_ilmnrev_deg3a2b0",
"locus_0119",
[
"6",
"33087504",
@@ -1036,7 +1036,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs59782580_ilmnrev_deg3a1b0",
"locus_0120",
[
"7",
"140836521",
@@ -1054,7 +1054,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs59782580_ilmnrev_F2BTindel",
"locus_0121",
[
"7",
"140836521",
@@ -1072,7 +1072,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs59782580_ilmnrev_F2BTindel_deg3a1b1",
"locus_0122",
[
"7",
"140836521",
@@ -1090,7 +1090,7 @@
],
[
"207895980019_R04C01",
"ilmnseq_rs3834939",
"locus_0114",
[
"12",
"21334835",
@@ -1108,7 +1108,7 @@
],
[
"207895980019_R04C01",
"ilmnseq_rs3834939_ilmnfwd_F2BTindel",
"locus_0115",
[
"12",
"21334835",
@@ -1128,7 +1128,7 @@
"ours_missing_haploid_Y": [
[
"207895980019_R03C01",
"rs373082162",
"locus_0067",
[
"Y",
"19466559",
@@ -1146,7 +1146,7 @@
],
[
"207895980019_R03C02",
"JHU_Y.14692226",
"locus_0069",
[
"Y",
"12580293",
@@ -1164,7 +1164,7 @@
],
[
"207895980019_R04C01",
"rs4020596",
"locus_0068",
[
"Y",
"5680808",
@@ -1182,7 +1182,7 @@
],
[
"207895980019_R11C02",
"rs5018209",
"locus_0061",
[
"Y",
"19428214",
@@ -1200,7 +1200,7 @@
],
[
"207895980019_R12C01",
"ilmnseq_rs538240449",
"locus_0063",
[
"Y",
"12030916",
@@ -1218,7 +1218,7 @@
],
[
"207895980019_R12C01",
"ilmnseq_rs537620655",
"locus_0064",
[
"Y",
"13331090",
@@ -1236,7 +1236,7 @@
],
[
"207895980035_R04C03",
"rs13304158",
"locus_0065",
[
"Y",
"9957467",
@@ -1254,7 +1254,7 @@
],
[
"207895980035_R04C03",
"exm1667692",
"locus_0066",
[
"Y",
"12816261",
@@ -1272,7 +1272,7 @@
],
[
"207895980035_R10C01",
"rs186564287",
"locus_0062",
[
"Y",
"14081208",
@@ -1292,7 +1292,7 @@
"ours_missing_het_in_haploid": [
[
"207895980019_R06C01",
"rs138003892",
"locus_0073",
[
"X",
"33006670",
@@ -1310,7 +1310,7 @@
],
[
"207895980019_R09C03",
"JHU_Y.6912991",
"locus_0123",
[
"Y",
"7044951",
@@ -1328,7 +1328,7 @@
],
[
"207895980019_R09C03",
"rs9786566",
"locus_0078",
[
"Y",
"7044951",
@@ -1346,7 +1346,7 @@
],
[
"207895980019_R15C02",
"rs1606778",
"locus_0075",
[
"X",
"79535086",
@@ -1364,7 +1364,7 @@
],
[
"207895980035_R03C03",
"JHU_X.22234615",
"locus_0077",
[
"X",
"22216499",
@@ -1382,7 +1382,7 @@
],
[
"207895980035_R05C03",
"rs12396137",
"locus_0083",
[
"X",
"7462384",
@@ -1400,7 +1400,7 @@
],
[
"207895980035_R05C03",
"rs4830772",
"locus_0084",
[
"X",
"7475195",
@@ -1418,7 +1418,7 @@
],
[
"207895980035_R05C03",
"rs146250304",
"locus_0072",
[
"X",
"68391913",
@@ -1436,7 +1436,7 @@
],
[
"207895980035_R09C03",
"rs28602676",
"locus_0074",
[
"MT",
"2690",
@@ -1454,7 +1454,7 @@
],
[
"207895980035_R11C03",
"ilmnseq_rs111298280",
"locus_0080",
[
"X",
"91616889",
@@ -1472,7 +1472,7 @@
],
[
"207895980035_R12C03",
"rs148519285",
"locus_0079",
[
"X",
"20830034",
@@ -1490,7 +1490,7 @@
],
[
"207895980035_R13C03",
"rs5979572",
"locus_0070",
[
"X",
"7467632",
@@ -1508,7 +1508,7 @@
],
[
"207895980035_R13C03",
"exm2273083",
"locus_0124",
[
"X",
"7478861",
@@ -1526,7 +1526,7 @@
],
[
"207895980035_R13C03",
"rs7887088",
"locus_0071",
[
"X",
"7478861",
@@ -1544,7 +1544,7 @@
],
[
"207895980035_R13C03",
"rs146250304",
"locus_0072",
[
"X",
"68391913",
@@ -1562,7 +1562,7 @@
],
[
"207895980035_R14C01",
"rs104894858",
"locus_0076",
[
"X",
"120442599",
@@ -1580,7 +1580,7 @@
],
[
"207895980042_R15C02",
"ilmnseq_rs553518378",
"locus_0082",
[
"Y",
"15734824",
@@ -1600,7 +1600,7 @@
"oracle_diploid_candidates_in_haploid_context": [
[
"207895980035_R11C03",
"ilmnseq_rs144970500.1_F2BT",
"locus_0125",
[
"X",
"22890860",
@@ -1618,7 +1618,7 @@
],
[
"207895980035_R11C03",
"ilmnseq_rs144970500.2_F2BT",
"locus_0126",
[
"X",
"22890860",
@@ -1636,5 +1636,6 @@
]
]
},
"unexplained": 0
"unexplained": 0,
"note": "Probe names from the vendor manifest are replaced by stable pseudonyms (locus_NNNN, shared by both oracle files); sample IDs, positions, alleles and all counts are unchanged."
}