TB-Profiler result

Run: SRR25827345
Summary

Run ID: SRR25827345

Sample name:

Date: 2024-04-16T06:39:49.651028

Number of reads: 7957714

Percentage reads mapped: 98.71

Median coverage: 272.0

Strain: lineage1.1.2;lineage2.2.1;lineage3.1.2;lineage4.8

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.33
lineage1.1.2 Indo-Oceanic RD239 0.17
lineage3.1.2 East-African-Indian RD750 0.26
lineage2 East-Asian RD105 0.28
lineage1.1 Indo-Oceanic RD239 0.18
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.3
lineage2.2 East-Asian (Beijing) RD105;RD207 0.29
lineage4 Euro-American None 0.18
lineage4.8 Euro-American (mainly T) RD219 0.16
lineage1 Indo-Oceanic RD239 0.22
lineage3.1 East-African-Indian RD750 0.26
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Gly132Ala Assoc w R
p.Asp63Gly Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
gid p.Tyr22* 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.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-37G>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid rplC p.Cys154Arg Assoc w R
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 0.24 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 7582 p.Asp94Gly missense_variant 0.18 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.45 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.19 linezolid Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.41 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.68 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.13 pyrazinamide Assoc w R
pncA 2289054 p.Asp63Gly missense_variant 0.21 pyrazinamide Assoc w R - Interim
eis 2715369 c.-37G>T upstream_gene_variant 0.15 kanamycin Assoc w R
gid 4408137 p.Tyr22* stop_gained 0.15 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
gyrB 5332 c.93C>T synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6112 p.Met291Ile missense_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8168 p.Glu289Asp missense_variant 0.13 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.2 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.18 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.78 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.31 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.12 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.29 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.2 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.66 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.31 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.17 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.24 rifampicin Not assoc w R
nusG 734658 c.405A>G synonymous_variant 0.18 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.2 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.34 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.22 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.29 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.76 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.17 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 764363 p.Gly332Ser missense_variant 0.13 rifampicin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 0.21 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.13 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.19 rifampicin Not assoc w R
rpoC 765862 p.Phe831Leu missense_variant 0.19 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775964 c.2517G>C synonymous_variant 0.24 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 0.86 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.25 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.21 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpR5 779243 p.Val85Gly missense_variant 0.14 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.23 linezolid Not assoc w R
rplC 801267 c.459A>G synonymous_variant 0.19 linezolid Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.83 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254591 c.-57C>T upstream_gene_variant 0.19 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.29 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.21 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.21 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.18 ethambutol
atpE 1460890 c.-155G>T upstream_gene_variant 0.19 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673406 c.-796C>G upstream_gene_variant 0.18 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
tsnR 1853843 p.Ser80Pro missense_variant 0.16 linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.19 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.21 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.84 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 0.19 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102791 c.252A>C synonymous_variant 0.2 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
katG 2153931 c.2181C>T synonymous_variant 0.26 isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.87 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.86 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.22 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670Leu missense_variant 0.24 pyrazinamide Not assoc w R
PPE35 2170785 c.-173T>C upstream_gene_variant 0.17 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.23 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.31 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.33 pyrazinamide
pncA 2289604 c.-363T>A upstream_gene_variant 0.25 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.2 isoniazid
eis 2715016 p.Arg106His missense_variant 0.17 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.21 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.38 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.34 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
Rv2477c 2784204 c.-162A>C upstream_gene_variant 0.3 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.22 capreomycin
Rv2681 2996912 c.174C>T synonymous_variant 0.2 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.23 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3065419 p.Arg258Leu missense_variant 0.17 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3065773 p.Glu140Gly missense_variant 0.17 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.84 cycloserine
ald 3086821 p.Met1? start_lost 0.16 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.29 ethionamide Uncertain significance
Rv3083 3448936 p.Tyr145Asp missense_variant 0.21 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.27 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.17 pyrazinamide Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.21 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.81 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.17 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.28 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640211 c.-332T>G upstream_gene_variant 0.12 clofazimine
pretomanid
delamanid
rpoA 3878575 c.-68C>A upstream_gene_variant 0.31 rifampicin Uncertain significance
rpoA 3878641 c.-135delG upstream_gene_variant 0.16 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.22 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.22 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.37 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.2 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.36 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 4240671 p.Thr270Ile missense_variant 0.27 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.24 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.33 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.27 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.21 ethambutol Not assoc w R
embA 4245417 p.Gly729Arg missense_variant 0.23 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.22 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.23 ethambutol
embB 4247429 c.916_918delATGinsGC frameshift_variant&missense_variant 0.32 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.29 ethambutol Not assoc w R
embB 4249485 p.Gly991Val missense_variant 0.22 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.28 ethambutol Not assoc w R
ubiA 4269102 c.732C>T synonymous_variant 0.2 ethambutol Not assoc w R - Interim
ubiA 4269296 p.Met180Val missense_variant 0.16 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.21 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.21 ethambutol Not assoc w R
ethA 4326878 p.Ala199Asp missense_variant 0.19 ethionamide
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 4338603 c.-82C>T upstream_gene_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.86 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.87 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.21 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.27 streptomycin Not assoc w R