TB-Profiler result

Run: SRR25340863
Summary

Run ID: SRR25340863

Sample name:

Date: 2024-10-05T08:02:35.891121

Number of reads: 11638031

Percentage reads mapped: 99.66

Median coverage: 326.0

Strain: lineage1.1.2;lineage4.8

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.11
lineage1.1 Indo-Oceanic RD239 0.1
lineage4 Euro-American None 0.87
lineage4.8 Euro-American (mainly T) RD219 0.88
lineage1 Indo-Oceanic RD239 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser428Arg Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.905C>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
rpoB 761090 p.Ser428Arg missense_variant 0.15 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rrs 1472750 n.905C>A non_coding_transcript_exon_variant 0.91 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.11 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.11 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.16 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.16 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.12 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.14 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.14 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.14 bedaquiline Uncertain significance
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.15 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.11 ethambutol
embR 1417580 c.-233T>C upstream_gene_variant 0.89 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.17 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.13 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.14 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2156563 c.-452G>A upstream_gene_variant 0.91 isoniazid Uncertain significance
PPE35 2167983 p.Gly877Asp missense_variant 0.15 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518132 c.18C>T synonymous_variant 0.14 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.19 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.86 capreomycin
Rv2681 2996912 c.174C>T synonymous_variant 0.13 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
Rv2752c 3066871 c.-680C>T upstream_gene_variant 0.87 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 0.15 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.11 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.18 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.15 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
alr 3840713 c.708C>T synonymous_variant 0.13 cycloserine
ddn 3987057 p.Arg72Trp missense_variant 0.12 pretomanid
delamanid Uncertain significance
panD 4044740 c.-459C>T upstream_gene_variant 0.14 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.15 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.14 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.16 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.14 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.15 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.14 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 4338603 c.-82C>T upstream_gene_variant 0.14 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.16 kanamycin
capreomycin
amikacin