TB-Profiler result

Run: SAMN02360591
Summary

Run ID: SAMN02360591

Sample name:

Date: 2024-10-05T06:11:49.607604

Number of reads: 1675954

Percentage reads mapped: 9.53

Median coverage: 35.0

Strain: lineage2.2.2

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
p.Ser140Asn Uncertain significance Mutation from literature
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Thr135Pro Assoc w R
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA c.820_830delGAGGGGTACGA Assoc w R
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
gyrA 7570 p.Ala90Val missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7572 p.Ser91Pro missense_variant 0.97 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.59 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
katG 2155693 p.Ser140Asn missense_variant 0.74 isoniazid Uncertain significance Mutation from literature
pncA 2288839 p.Thr135Pro missense_variant 0.96 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.95 para-aminosalicylic_acid Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol Assoc w R
ethA 4326643 c.820_830delGAGGGGTACGA frameshift_variant 0.97 ethionamide Assoc w R
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 762881 p.Met1025Ile missense_variant 0.26 rifampicin
rpoC 762893 c.-477C>T upstream_gene_variant 0.44 rifampicin
rpoC 762896 c.-474G>C upstream_gene_variant 0.5 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.51 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.51 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.51 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.49 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.49 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.51 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.51 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.36 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 762998 c.-372G>A upstream_gene_variant 0.19 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764329 c.960C>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764338 p.Glu323Asp missense_variant 0.51 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.5 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.51 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.54 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.56 rifampicin
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764398 c.1029G>C synonymous_variant 0.58 rifampicin
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 764410 c.1041G>T synonymous_variant 0.58 rifampicin
rpoC 764428 c.1059G>T synonymous_variant 0.44 rifampicin
rpoC 764434 c.1065A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.21 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764656 c.1287C>G synonymous_variant 0.13 rifampicin
rpoC 764723 p.Phe452Leu missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781406 c.-154_-153insC upstream_gene_variant 1.0 streptomycin Uncertain significance
Rv1129c 1254136 p.Glu133Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.68 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.67 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.64 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.61 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.59 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.47 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.47 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.36 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.33 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.29 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.25 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.5 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473129 n.1286delG non_coding_transcript_exon_variant 0.3 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.7 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.74 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rpsA 1833909 p.Asp123Ala missense_variant 1.0 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834972 c.1431C>T synonymous_variant 0.92 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155600 p.Cys171Val missense_variant 0.56 isoniazid
katG 2155613 p.Phe167Leu missense_variant 0.61 isoniazid
katG 2155614 c.498T>C synonymous_variant 0.61 isoniazid
katG 2155617 p.Ile165Met missense_variant 0.65 isoniazid
katG 2155626 c.486G>C synonymous_variant 0.72 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.77 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.76 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.74 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.77 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.77 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.81 isoniazid
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.75 isoniazid Not assoc w R - Interim
katG 2155704 c.408C>T synonymous_variant 0.76 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.76 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.73 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.69 isoniazid
katG 2155735 p.Met126Gln missense_variant 0.66 isoniazid
katG 2155737 c.375C>T synonymous_variant 0.69 isoniazid
katG 2155741 p.Gly124Ala missense_variant 0.67 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.68 isoniazid
katG 2155765 p.His116Thr missense_variant 0.59 isoniazid
katG 2155782 c.330C>G synonymous_variant 0.28 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyA 3073979 p.Gln165* stop_gained 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840952 p.Lys157Glu missense_variant 0.94 cycloserine
embC 4241465 p.Phe535Leu missense_variant 0.96 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.97 streptomycin Not assoc w R