TB-Profiler result

Run: ERR4831841
Summary

Run ID: ERR4831841

Sample name:

Date: 2024-10-05T12:45:04.109001

Number of reads: 1690482

Percentage reads mapped: 92.8

Median coverage: 43.0

Strain: lineage2.2.1;lineage4.4.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.05
lineage2.2 East-Asian (Beijing) RD105;RD207 0.08
lineage4 Euro-American None 0.91
lineage4.4 Euro-American None 0.91
lineage4.4.2 Euro-American None 0.9
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.102delG Assoc w R
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
gid 4408100 c.102delG frameshift_variant 0.98 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
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
rpoB 760235 c.429T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760244 c.438G>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoB 761147 c.1341C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761171 c.1365C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761186 p.Glu460Asp missense_variant 0.11 rifampicin Uncertain significance
rpoB 761189 c.1383T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761198 c.1392G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.35 rifampicin Not assoc w R
rpoC 763915 c.546C>T synonymous_variant 0.87 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 779054 p.Gln22Arg missense_variant 0.89 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303047 c.117G>A synonymous_variant 0.93 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
embR 1416989 c.358delA frameshift_variant 0.97 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833760 c.219C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1834177 c.636A>C synonymous_variant 0.11 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 2063106 c.1623G>A synonymous_variant 0.13 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2221889 p.Val426Ile missense_variant 0.18 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 2517917 c.-198G>C upstream_gene_variant 0.13 isoniazid
Rv2752c 3066099 p.Met31Ile missense_variant 0.83 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.89 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.25 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.24 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038612 p.Asn698Ser missense_variant 0.98 pyrazinamide
glpK 4139183 c.572dupG frameshift_variant 0.6 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.83 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.94 ethambutol Uncertain significance
ubiA 4268928 c.906C>T synonymous_variant 0.81 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.95 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 0.95 kanamycin
capreomycin
amikacin
gid 4407927 p.Glu92Asp missense_variant 0.14 streptomycin Not assoc w R