TB-Profiler result

Run: SRR1049623
Summary

Run ID: SRR1049623

Sample name:

Date: 2024-10-04T19:24:08.402053

Number of reads: 2539286

Percentage reads mapped: 65.6

Median coverage: 54.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1 Euro-American (S-type) None 0.84
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.99
lineage4.4 Euro-American None 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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.390_391dupGG Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.94 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
gyrB 5195 c.-45C>G upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
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 734851 p.Thr200Ala missense_variant 0.98 rifampicin Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762917 c.3111C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.12 rifampicin
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.11 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.11 rifampicin 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 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.43 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.39 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.32 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.25 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.22 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.37 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.25 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.42 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid Uncertain significance
ndh 2102990 p.Val18Ala missense_variant 1.0 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 0.95 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2746923 p.Gly226Ser missense_variant 1.0 para-aminosalicylic_acid
Rv2681 2997212 c.474A>C synonymous_variant 1.0 capreomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
glpK 4138687 p.Gly357Ser missense_variant 0.15 levofloxacin
moxifloxacin
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol
glpK 4139183 c.572dupG frameshift_variant 0.81 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embA 4243692 p.Gly154Ser missense_variant 1.0 ethambutol Uncertain significance
embB 4246904 p.Val131Met missense_variant 0.9 ethambutol Uncertain significance
ethA 4328252 c.-779T>G upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407758 p.Ser149Arg missense_variant 1.0 streptomycin Uncertain significance