TB-Profiler result

Run: SRR7755733
Summary

Run ID: SRR7755733

Sample name:

Date: 2024-04-16T06:24:27.607279

Number of reads: 1534030

Percentage reads mapped: 31.57

Median coverage: 31.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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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
lineage4.3.3 Euro-American (LAM) RD115 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Tyr319Ser Assoc w R
pyrazinamide pncA p.Asp63Ala Assoc w R
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.97 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289054 p.Asp63Ala missense_variant 1.0 pyrazinamide Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 1.0 ethambutol 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
dnaA 698 p.Arg233Gln missense_variant 1.0 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 8040 p.Gly247Ser missense_variant 0.95 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
rpoC 764667 p.Gly433Ala missense_variant 1.0 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
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
fbiC 1303095 c.165G>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304962 p.Trp678Gly missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.54 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 0.54 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472135 n.290C>G non_coding_transcript_exon_variant 0.58 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.6 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.41 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.49 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.49 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.72 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.72 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.72 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.71 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.71 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.72 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.71 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.71 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.71 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475499 n.1842C>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475522 n.1865A>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid Uncertain significance
rrl 1475526 n.1869C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475528 n.1871T>G non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475553 n.1896G>C non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475576 n.1919C>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.62 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834836 p.Met432Thr missense_variant 1.0 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
katG 2156196 c.-85C>T upstream_gene_variant 1.0 isoniazid 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
kasA 2518919 p.Gly269Ser missense_variant 0.96 isoniazid
folC 2746340 p.Ala420Val missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782767 p.Val426Met missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ribD 2986827 c.-12G>A upstream_gene_variant 1.0 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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