TB-Profiler result

Run: SRR13861235
Summary

Run ID: SRR13861235

Sample name:

Date: 2024-04-15T07:52:45.732146

Number of reads: 2629915

Percentage reads mapped: 43.88

Median coverage: 90.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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 katG p.Gly234Glu Uncertain significance Mutation from literature
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
katG 2155411 p.Gly234Glu missense_variant 1.0 isoniazid 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
gyrA 7760 c.459C>T synonymous_variant 0.12 levofloxacin
moxifloxacin
Rv0010c 13524 p.Gly12Ala missense_variant 1.0 isoniazid
mshA 576259 c.912C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ccsA 620690 p.Val267Glu missense_variant 0.89 capreomycin
amikacin
kanamycin
Rv0565c 657622 c.-152G>A upstream_gene_variant 0.94 ethionamide
rpoB 759805 c.-2T>C upstream_gene_variant 1.0 rifampicin
rpoB 761961 p.Pro719Thr missense_variant 0.88 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764895 p.Ile509Thr missense_variant 0.92 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.14 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.14 rifampicin
rpoC 766738 c.3369G>T synonymous_variant 0.16 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.15 rifampicin
rpoC 766801 c.3432C>A synonymous_variant 0.13 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
mmpL5 777574 p.Phe303Leu missense_variant 1.0 clofazimine
bedaquiline
mmpL5 777578 c.903C>G synonymous_variant 1.0 clofazimine
bedaquiline
mmpL5 778982 c.-502A>C upstream_gene_variant 1.0 clofazimine
bedaquiline
rplC 801169 p.Lys121* stop_gained 0.93 linezolid
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476479 n.2822T>G non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rpsA 1834375 c.834G>A synonymous_variant 0.13 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.15 pyrazinamide
tlyA 1918432 p.Pro165Thr missense_variant 1.0 capreomycin
ndh 2101769 p.Arg425His missense_variant 1.0 ethionamide
delamanid
isoniazid Uncertain significance
katG 2155508 p.Ala202Ser missense_variant 1.0 isoniazid Uncertain significance
pncA 2289474 c.-233C>G upstream_gene_variant 1.0 pyrazinamide
kasA 2518519 c.405G>C synonymous_variant 0.13 isoniazid
kasA 2518540 c.426T>G synonymous_variant 0.14 isoniazid
folC 2746862 p.Leu246Arg missense_variant 1.0 para-aminosalicylic_acid
folC 2747268 p.Asp111His missense_variant 0.96 para-aminosalicylic_acid
Rv2752c 3065109 c.1083A>G synonymous_variant 0.99 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066839 c.-648A>G upstream_gene_variant 0.13 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
whiB7 3568816 c.-137C>T upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
whiB7 3569222 c.-543G>A upstream_gene_variant 0.99 streptomycin
amikacin
kanamycin
lpqB 3624508 p.Ile135Val missense_variant 0.97 bedaquiline
rifampicin
mtrB 3625247 p.Arg456Pro missense_variant 0.97 bedaquiline
rifampicin
rpoA 3878049 c.459G>C synonymous_variant 0.14 rifampicin
rpoA 3878055 c.453A>G synonymous_variant 0.15 rifampicin
rpoA 3878061 c.447G>C synonymous_variant 0.16 rifampicin
rpoA 3878067 c.441C>G synonymous_variant 0.14 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.15 rifampicin
rpoA 3878082 c.426T>C synonymous_variant 0.14 rifampicin
clpC1 4038468 p.Asp746Gly missense_variant 0.89 pyrazinamide
clpC1 4038536 c.2169C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039085 c.1620A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039090 c.1615C>T synonymous_variant 0.14 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039103 c.1602T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.14 pyrazinamide
clpC1 4039172 c.1533A>G synonymous_variant 0.15 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.14 pyrazinamide
clpC1 4040148 p.Lys186Ile missense_variant 0.96 pyrazinamide
embC 4240125 p.Cys88Tyr missense_variant 0.95 ethambutol
embC 4240726 c.864G>C synonymous_variant 0.13 ethambutol Not assoc w R - Interim
embC 4240780 c.918T>C synonymous_variant 0.15 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.16 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.16 ethambutol
embB 4248085 c.1572T>C synonymous_variant 0.15 ethambutol
embB 4248097 c.1584C>G synonymous_variant 0.16 ethambutol
embB 4248118 c.1605T>C synonymous_variant 0.13 ethambutol
embB 4248157 c.1644A>G synonymous_variant 0.14 ethambutol Not assoc w R - Interim
embB 4248208 p.Ser565Arg missense_variant 0.15 ethambutol
embB 4248220 c.1707A>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
embB 4248241 c.1728C>T synonymous_variant 0.19 ethambutol
embB 4248265 c.1752C>T synonymous_variant 0.16 ethambutol
embB 4248266 c.1753C>T synonymous_variant 0.17 ethambutol
embB 4248277 c.1764G>C synonymous_variant 0.15 ethambutol
ethR 4327643 p.Thr32Ile missense_variant 0.99 ethionamide