TB-Profiler result

Run: SRR13861333
Summary

Run ID: SRR13861333

Sample name:

Date: 2024-10-05T03:36:37.440314

Number of reads: 1408790

Percentage reads mapped: 35.25

Median coverage: 48.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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 375 p.Asp125Glu missense_variant 1.0 isoniazid
dnaA 1209 c.1209C>T synonymous_variant 0.14 isoniazid Not assoc w R - Interim
dnaA 1220 p.Asn407Ser missense_variant 0.14 isoniazid
dnaA 1230 c.1230A>G synonymous_variant 0.14 isoniazid
gyrB 4996 c.-244A>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 5258 p.Lys7* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin
gyrB 7122 c.1883_1884insA frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
Rv0010c 13577 c.-19G>T upstream_gene_variant 1.0 isoniazid
mmaA3 738206 c.-57G>T upstream_gene_variant 1.0 isoniazid
rpoB 762101 c.2295C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.14 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.16 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.18 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.21 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.15 rifampicin
rpoB 763085 c.3279C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.13 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.13 rifampicin
rpoC 766484 p.Val1039Ile missense_variant 0.13 rifampicin Uncertain significance
rpoC 766492 c.3123T>C synonymous_variant 0.14 rifampicin
rpoC 766495 c.3126C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766522 c.3153C>G synonymous_variant 0.17 rifampicin
rpoC 766528 c.3159T>C synonymous_variant 0.14 rifampicin
rpoC 766531 c.3162G>T synonymous_variant 0.14 rifampicin
rpoC 766543 c.3174C>T synonymous_variant 0.15 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.15 rifampicin
mmpL5 776374 p.Arg703Cys missense_variant 1.0 bedaquiline
clofazimine
mmpR5 779126 p.Cys46Phe missense_variant 1.0 bedaquiline
clofazimine
rplC 801447 p.Lys213Asn missense_variant 0.98 linezolid
Rv1129c 1253197 c.1338C>A synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1253317 c.1218G>A synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1253639 p.Leu299* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
fbiC 1303004 p.Ala25Glu missense_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1303171 p.Arg81Trp missense_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1303517 p.Met196Thr missense_variant 1.0 pretomanid
delamanid
clofazimine
Rv1258c 1407597 c.-257C>G upstream_gene_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rpsA 1833940 c.399C>G synonymous_variant 0.22 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.21 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834640 p.Glu367* stop_gained 0.93 pyrazinamide Uncertain significance
bacA 2064395 p.Thr112Pro missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
bacA 2064589 c.139delT frameshift_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
ndh 2103004 c.39T>G synonymous_variant 1.0 isoniazid
delamanid
ethionamide
PPE35 2170453 p.Gly54Ser missense_variant 1.0 pyrazinamide
Rv1979c 2223326 c.-162C>T upstream_gene_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223365 c.-201C>A upstream_gene_variant 1.0 bedaquiline
clofazimine
pncA 2288748 p.Ala165Asp missense_variant 1.0 pyrazinamide
kasA 2518474 p.Glu120Asp missense_variant 0.95 isoniazid
Rv2477c 2783116 c.927T>C synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783140 c.903C>G synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyX 3067529 c.417C>G synonymous_variant 0.96 para-aminosalicylic_acid
thyA 3073764 c.708T>C synonymous_variant 1.0 para-aminosalicylic_acid
thyA 3073862 p.Gly204Ser missense_variant 0.96 para-aminosalicylic_acid
thyA 3073963 p.Leu170Gln missense_variant 0.94 para-aminosalicylic_acid
fbiD 3339357 c.240G>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
Rv3083 3448352 c.-152G>C upstream_gene_variant 1.0 ethionamide
Rv3083 3449624 p.Lys374Met missense_variant 1.0 ethionamide
Rv3083 3449919 c.1416C>A synonymous_variant 1.0 ethionamide
fbiB 3642227 p.Gln231His missense_variant 1.0 pretomanid
delamanid
clofazimine
fbiB 3642581 c.1047A>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
embA 4244641 p.Val470Gly missense_variant 1.0 ethambutol
embA 4245197 c.1965C>T synonymous_variant 0.95 ethambutol Not assoc w R - Interim
embB 4246641 p.Ala43Glu missense_variant 1.0 ethambutol
embB 4247233 p.Asp240Glu missense_variant 1.0 ethambutol
ethA 4327035 p.Tyr147Asp missense_variant 1.0 ethionamide
ethR 4327923 p.Gln125His missense_variant 1.0 ethionamide