TB-Profiler result

Run: ERR161149
Summary

Run ID: ERR161149

Sample name:

Date: 2024-04-15T04:03:56.494412

Number of reads: 2987848

Percentage reads mapped: 92.32

Median coverage: 65.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 0.98
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
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
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
dnaA 1191 c.1191T>C synonymous_variant 0.14 isoniazid
dnaA 1215 c.1215C>T synonymous_variant 0.15 isoniazid
dnaA 1220 p.Asn407Ser missense_variant 0.14 isoniazid
dnaA 1230 c.1230A>G synonymous_variant 0.15 isoniazid
dnaA 1242 c.1242G>C synonymous_variant 0.14 isoniazid
dnaA 1254 c.1254T>G synonymous_variant 0.14 isoniazid
dnaA 1255 p.Ala419Thr missense_variant 0.86 isoniazid Uncertain significance
gyrB 6140 p.Val301Leu missense_variant 0.89 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 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
nusG 734475 c.222T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
nusG 734481 c.228C>T synonymous_variant 0.12 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
nusG 734559 c.306T>C synonymous_variant 0.12 rifampicin
rpoB 762131 c.2325C>G synonymous_variant 0.14 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.18 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762197 c.2391C>T synonymous_variant 0.18 rifampicin
rpoB 762489 p.Val895Leu missense_variant 0.12 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764203 c.834G>T synonymous_variant 0.15 rifampicin
rpoC 764206 c.837T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764213 p.Arg282Lys missense_variant 0.15 rifampicin Uncertain significance
rpoC 764257 c.888G>C synonymous_variant 0.16 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765658 c.2289C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765784 c.2415C>G synonymous_variant 0.12 rifampicin
rpoC 765811 c.2442T>G synonymous_variant 0.15 rifampicin
rpoC 765826 c.2457T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.13 rifampicin
rpoC 767158 c.3789T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767167 c.3798C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpsA 1833703 c.162C>T synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1833724 c.183C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833727 c.186G>T synonymous_variant 0.14 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834294 c.753G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834303 c.762T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834612 c.1071G>A synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834618 c.1077G>T synonymous_variant 0.15 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.16 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834654 c.1113G>A synonymous_variant 0.15 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.14 pyrazinamide
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783140 c.903C>G synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.88 para-aminosalicylic_acid
thyA 3073892 c.580T>C synonymous_variant 0.12 para-aminosalicylic_acid
thyA 3073917 c.555C>G synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073925 c.547T>C synonymous_variant 0.13 para-aminosalicylic_acid
thyA 3073929 c.543T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073953 c.519T>G synonymous_variant 0.17 para-aminosalicylic_acid
thyA 3073958 c.514C>T synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073959 c.513T>C synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3073977 c.495A>G synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3073989 c.483T>C synonymous_variant 0.16 para-aminosalicylic_acid
thyA 3074001 c.471C>G synonymous_variant 0.13 para-aminosalicylic_acid
thyA 3074004 c.468T>C synonymous_variant 0.12 para-aminosalicylic_acid
thyA 3074010 c.462C>G synonymous_variant 0.13 para-aminosalicylic_acid
thyA 3074120 c.352T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3074121 c.351T>C synonymous_variant 0.13 para-aminosalicylic_acid
thyA 3074127 c.345G>C synonymous_variant 0.13 para-aminosalicylic_acid
thyA 3074130 c.342G>C synonymous_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.98 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
rpoA 3877920 c.588G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.19 rifampicin
rpoA 3877962 c.546G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
ddn 3986636 c.-208C>G upstream_gene_variant 0.15 delamanid
pretomanid
ddn 3986645 c.-199G>A upstream_gene_variant 0.13 delamanid
pretomanid
ddn 3986648 c.-196C>G upstream_gene_variant 0.13 delamanid
pretomanid
ddn 3986665 c.-179G>C upstream_gene_variant 0.13 delamanid
pretomanid
ddn 3986667 c.-177_-176delCTinsAC upstream_gene_variant 0.13 delamanid
pretomanid
clpC1 4038287 c.2418C>T synonymous_variant 0.98 pyrazinamide Not assoc w R
clpC1 4039298 c.1407T>C synonymous_variant 0.12 pyrazinamide
clpC1 4039577 c.1128T>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4039610 c.1095G>C synonymous_variant 0.12 pyrazinamide
glpK 4138535 c.1221T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R