TB-Profiler result

Run: ERR4819377
Summary

Run ID: ERR4819377

Sample name:

Date: 2024-03-26T22:51:07.542556

Number of reads: 1154320

Percentage reads mapped: 79.44

Median coverage: 22.0

Strain: lineage3.1.2.1;lineage4

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.96
lineage3.1.2 East-African-Indian RD750 0.97
lineage4 Euro-American None 0.08
lineage3.1.2.1 East-African-Indian RD750 0.97
lineage3.1 East-African-Indian RD750 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.888G>A Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance Mutation from literature
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 0.83 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 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.93 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.95 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 767250 p.Ser1294Asn missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.9 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.96 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 0.94 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.97 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1407511 c.-171T>C upstream_gene_variant 0.95 streptomycin
isoniazid
pyrazinamide
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.99 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.99 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.67 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.61 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.41 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.61 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
fabG1 1673319 c.-121A>C upstream_gene_variant 0.96 ethionamide
isoniazid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.95 capreomycin Not assoc w R
bacA 2064415 p.Gly105Asp missense_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.88 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.95 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.91 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.93 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840320 c.1101G>T synonymous_variant 1.0 cycloserine
clpC1 4040886 c.-182T>G upstream_gene_variant 1.0 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.96 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.96 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.93 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R