TB-Profiler result

Run: SRR25827452
Summary

Run ID: SRR25827452

Sample name:

Date: 2024-10-04T06:25:41.685552

Number of reads: 6755812

Percentage reads mapped: 93.95

Median coverage: 228.0

Strain: lineage1.1.2;lineage2.2.1;lineage4.2.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.37
lineage1.1.2 Indo-Oceanic RD239 0.16
lineage2 East-Asian RD105 0.46
lineage4.2 Euro-American None 0.39
lineage1.1 Indo-Oceanic RD239 0.15
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.45
lineage2.2 East-Asian (Beijing) RD105;RD207 0.46
lineage4 Euro-American None 0.36
lineage1 Indo-Oceanic RD239 0.16
lineage4.2.2.2 Euro-American (Ural) None 0.36
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
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Gln853Pro Uncertain significance Mutation from literature
pyrazinamide pncA p.Leu159Arg Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
rpoB 761155 p.Ser450Leu missense_variant 0.51 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.38 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.52 isoniazid Assoc w R High-level resistance
pncA 2288766 p.Leu159Arg missense_variant 0.31 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.28 para-aminosalicylic_acid Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 0.22 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.23 ethambutol Assoc w R
embB 4249071 p.Gln853Pro missense_variant 0.23 ethambutol 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
gyrB 6112 p.Met291Ile missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7283 c.-19G>T upstream_gene_variant 0.26 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 8688 p.Ala463Ser missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.2 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
Rv0010c 13298 p.Ile87Met missense_variant 0.15 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.24 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.67 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574539 c.-809C>G upstream_gene_variant 0.38 isoniazid
ethionamide
mshA 575907 p.Ala187Val missense_variant 0.5 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.25 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.43 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.45 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.42 ethionamide Uncertain significance
Rv0565c 657425 p.Gly16Ser missense_variant 0.41 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.22 ethionamide
rpoB 759546 c.-261A>G upstream_gene_variant 0.23 rifampicin Not assoc w R
rpoB 761006 c.1200C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761213 c.1407G>C synonymous_variant 0.15 rifampicin
rpoB 761219 c.1413G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.15 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.61 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.15 rifampicin
rpoC 763884 p.Ala172Val missense_variant 0.16 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 764461 c.1092A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764510 c.1141C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.19 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764554 c.1185C>T synonymous_variant 0.17 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.18 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.17 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764652 p.Ser428Trp missense_variant 0.15 rifampicin
rpoC 764858 c.1489T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765171 p.Pro601Leu missense_variant 0.16 rifampicin Not assoc w R
rpoC 765700 c.2331T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766630 c.3261G>C synonymous_variant 0.14 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.15 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.15 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.15 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.14 rifampicin
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 0.65 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.5 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.15 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpS5 778883 p.Ala8Val missense_variant 0.16 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.31 linezolid
Rv1129c 1253930 p.Phe202Tyr missense_variant 0.37 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.66 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254583 c.-49A>G upstream_gene_variant 0.36 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.4 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406878 p.Ile155Val missense_variant 0.18 streptomycin
pyrazinamide
isoniazid
embR 1417554 c.-207C>G upstream_gene_variant 0.15 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.2 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.5 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.2 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.17 linezolid Not assoc w R
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
bacA 2063685 c.1044G>A synonymous_variant 0.37 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.35 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.61 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.69 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.19 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.19 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 0.15 isoniazid
pepQ 2859659 p.Ala254Thr missense_variant 0.47 bedaquiline
clofazimine Uncertain significance
Rv2752c 3064632 c.1560C>T synonymous_variant 0.16 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 3066280 c.-89C>T upstream_gene_variant 0.44 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.35 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.17 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.46 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.2 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.41 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878416 p.Gly31Ala missense_variant 0.22 rifampicin Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.15 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 4239593 c.-270G>A upstream_gene_variant 0.2 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.19 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.26 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.47 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.18 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.17 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.2 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.22 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.29 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.18 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.15 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 0.6 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.31 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.2 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.39 streptomycin Not assoc w R