TB-Profiler result

Run: SRR11444077
Summary

Run ID: SRR11444077

Sample name:

Date: 2024-04-15T19:32:59.910964

Number of reads: 4934918

Percentage reads mapped: 88.42

Median coverage: 111.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 1.0
lineage4.6.2 Euro-American RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) RD726 1.0
lineage4 Euro-American None 1.0
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 769 p.Ala257Thr missense_variant 0.32 isoniazid 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 8897 c.1596T>C synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8909 c.1608C>T synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 8915 c.1614A>G synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13637 c.-79C>T upstream_gene_variant 0.33 isoniazid Uncertain significance
rpoB 760196 c.390C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 760235 c.429T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760244 c.438G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760310 c.504G>C synonymous_variant 0.14 rifampicin
rpoB 760376 p.Asp190Glu missense_variant 0.12 rifampicin Uncertain significance
rpoB 760430 c.624T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 760460 c.654G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761264 c.1458C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>A synonymous_variant 0.12 rifampicin
rpoC 763675 c.306C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>T synonymous_variant 0.12 rifampicin
rpoC 764746 c.1377G>T 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
mmpL5 778298 c.183G>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254144 p.Thr131Pro missense_variant 0.37 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833838 c.297G>C synonymous_variant 0.11 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.11 pyrazinamide
rpsA 1833859 c.318C>G synonymous_variant 0.11 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.12 pyrazinamide
rpsA 1833994 c.453G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.15 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
bacA 2063187 c.1542C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.96 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289037 p.Pro69Ser missense_variant 0.99 pyrazinamide Uncertain significance
Rv2680 2996208 p.Ala35Asp missense_variant 1.0 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 1.0 para-aminosalicylic_acid
Rv3083 3448567 p.His22Asp missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612571 c.546C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
mtrA 3627068 c.282T>C synonymous_variant 0.11 bedaquiline
rifampicin Not assoc w R - Interim
clpC1 4039682 c.1023C>G synonymous_variant 0.12 pyrazinamide
embC 4240783 c.921G>C synonymous_variant 0.13 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.12 ethambutol
embC 4242550 c.2688C>G synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 1.0 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 0.89 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