TB-Profiler result

Run: SRR7535074
Summary

Run ID: SRR7535074

Sample name:

Date: 2024-10-05T13:18:04.796342

Number of reads: 1703990

Percentage reads mapped: 10.04

Median coverage: 36.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 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
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
fgd1 491742 c.960T>C synonymous_variant 0.91 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
hadA 731858 c.-72G>C upstream_gene_variant 1.0 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.97 rifampicin Not assoc w R
rpoB 762894 c.3088C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762911 p.Ile1035Met missense_variant 0.36 rifampicin
rpoB 762923 c.3117C>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 762932 c.-438G>T upstream_gene_variant 0.36 rifampicin
rpoB 762939 p.Met1045Leu missense_variant 0.38 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.38 rifampicin Uncertain significance
rpoC 762947 c.-423C>G upstream_gene_variant 0.38 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 762989 c.3183G>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 762998 c.-372G>A upstream_gene_variant 0.2 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764854 c.1485G>C synonymous_variant 0.15 rifampicin
rpoC 764858 p.Leu497Met missense_variant 0.15 rifampicin
rpoC 764869 c.1500C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>T synonymous_variant 0.17 rifampicin
rpoC 764878 c.1509C>G synonymous_variant 0.16 rifampicin
rpoC 764887 c.1518G>T synonymous_variant 0.19 rifampicin
rpoC 764893 c.1524T>C synonymous_variant 0.26 rifampicin
rpoC 764905 c.1536C>T synonymous_variant 0.35 rifampicin
rpoC 764911 c.1542A>C synonymous_variant 0.33 rifampicin
rpoC 764914 p.Met515Ile missense_variant 0.32 rifampicin Uncertain significance
rpoC 764918 p.Val517Ile missense_variant 0.33 rifampicin
rpoC 764939 c.1570C>T synonymous_variant 0.28 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.54 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.89 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.85 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.86 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.85 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.82 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.81 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.8 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.79 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.78 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472824 n.979T>C non_coding_transcript_exon_variant 0.35 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.46 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.77 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.87 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 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.89 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 0.88 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.61 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.58 capreomycin Not assoc w R
linezolid Uncertain significance
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 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155449 c.663C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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
pncA 2289047 c.195C>T synonymous_variant 0.98 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841296 p.Leu42Pro missense_variant 1.0 cycloserine
alr 3841473 c.-53G>A upstream_gene_variant 1.0 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R