TB-Profiler result

Run: SRR998828
Summary

Run ID: SRR998828

Sample name:

Date: 2024-10-04T06:10:39.705976

Number of reads: 3481927

Percentage reads mapped: 99.45

Median coverage: 80.0

Strain: lineage4.6.2.2;lineage6.3.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.86
lineage4.6.2 Euro-American RD726 0.89
lineage6.3 West-Africa 2 RD702 0.14
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.86
lineage4 Euro-American None 0.88
lineage6.3.1 West-Africa 2 RD702 0.11
lineage6 West-Africa 2 RD702 0.14
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)
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ala146Val Assoc w R
streptomycin rrs n.514A>C 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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
gyrA 7570 p.Ala90Val missense_variant 0.16 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 0.95 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.81 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.85 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)
pncA 2288805 p.Ala146Val missense_variant 0.92 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.82 ethambutol 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
gyrA 9591 p.Gly764Arg missense_variant 0.19 levofloxacin Uncertain significance
moxifloxacin
Rv0010c 13460 c.99T>C synonymous_variant 0.19 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.16 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.18 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 619628 c.-263G>A upstream_gene_variant 0.14 kanamycin
capreomycin
amikacin
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.13 ethionamide
nusG 734151 c.-103G>C upstream_gene_variant 0.12 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.16 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.89 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 0.11 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 0.92 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.14 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.16 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.2 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.14 isoniazid Not assoc w R
ethionamide Uncertain significance
rpsA 1834564 c.1023C>T synonymous_variant 0.93 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
bacA 2062922 p.Ile603Val missense_variant 0.17 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063187 c.1542C>T synonymous_variant 0.92 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2153986 p.Glu709Ala missense_variant 0.92 isoniazid Uncertain significance
katG 2155503 c.609C>T synonymous_variant 0.12 isoniazid Not assoc w R
katG 2156366 c.-255G>A upstream_gene_variant 0.2 isoniazid
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.86 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.12 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2222852 p.Ala105Thr missense_variant 0.14 bedaquiline Uncertain significance
clofazimine Uncertain significance
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
folC 2746873 p.Met242Ile missense_variant 0.8 para-aminosalicylic_acid
Rv2680 2996208 p.Ala35Asp missense_variant 0.82 capreomycin Uncertain significance
Rv2752c 3064747 p.Gly482Val missense_variant 0.84 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.1 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.8 ethionamide Uncertain significance
Rv3083 3449781 c.1278G>A synonymous_variant 0.17 ethionamide Not assoc w R - Interim
Rv3236c 3613354 c.-238G>T upstream_gene_variant 0.15 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 0.19 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.17 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877696 p.Thr271Ile missense_variant 0.17 rifampicin Uncertain significance
glpK 4138983 p.Val258Gly missense_variant 0.21 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4241843 p.Leu661Ile missense_variant 0.17 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.17 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.3 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.15 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.85 ethambutol Not assoc w R
aftB 4268477 c.360C>T synonymous_variant 0.13 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.11 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.13 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.14 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.18 ethionamide Uncertain significance
ethA 4326739 c.735C>G synonymous_variant 0.9 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
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 0.25 streptomycin Not assoc w R