TB-Profiler result

Run: ERR751338
Summary

Run ID: ERR751338

Sample name:

Date: 2024-10-05T03:24:04.175699

Number of reads: 1683032

Percentage reads mapped: 29.78

Median coverage: 35.0

Strain: lineage5.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage5.1.1 West-Africa 1 RD711 1.0
lineage5 West-Africa 1 RD711 1.0
lineage5.1 West-Africa 1 RD711 0.74
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 rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin 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 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin 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 9143 c.1842T>C synonymous_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
gyrA 9566 c.2265C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13579 c.-21G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 1.0 isoniazid
rpoB 762939 p.Met1045Leu missense_variant 0.18 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.18 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763280 c.3474C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1407273 p.Asp23Val missense_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.49 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 0.7 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.7 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.69 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.64 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 0.62 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.61 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.55 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.43 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472338 n.493A>T non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.19 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 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472379 n.534T>A non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.18 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 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.61 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.61 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.64 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.75 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.75 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 0.74 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 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.62 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.3 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.78 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.73 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.63 capreomycin
linezolid
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.49 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
inhA 1673338 c.-864G>A upstream_gene_variant 1.0 isoniazid
ethionamide
tsnR 1853565 c.-41G>A upstream_gene_variant 1.0 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
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2064844 c.-116G>C upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
ndh 2101840 c.1203G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
ndh 2101921 c.1122G>A synonymous_variant 0.98 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
ndh 2103112 c.-70G>T upstream_gene_variant 1.0 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
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 2290062 c.-821G>A upstream_gene_variant 1.0 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
folC 2747784 c.-186C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0 cycloserine
Rv3083 3449644 p.Ala381Thr missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840932 c.489C>T synonymous_variant 1.0 cycloserine
rpoA 3878493 c.15G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
ddn 3986987 c.144G>T synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
ddn 3987180 p.Asp113Asn missense_variant 1.0 pretomanid
delamanid Uncertain significance
clpC1 4040462 c.243C>T synonymous_variant 1.0 pyrazinamide
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138303 p.Lys485Gln missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138377 p.Val460Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139131 p.Glu209Lys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 1.0 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 1.0 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269693 c.141C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ethA 4326567 p.Arg303Trp missense_variant 1.0 ethionamide
ethA 4326928 c.546C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4327103 p.Gly124Asp missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338547 c.-26A>G upstream_gene_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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