TB-Profiler result

Run: ERR4831618
Summary

Run ID: ERR4831618

Sample name:

Date: 2024-03-26T13:56:31.814196

Number of reads: 948709

Percentage reads mapped: 80.06

Median coverage: 28.0

Strain: lineage2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.1 East-Asian (non-Beijing) 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 rpoB p.His445Arg Assoc w R
c.1342_1344delCGAinsGT Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
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
rpoB 761140 p.His445Arg missense_variant 0.83 rifampicin Assoc w R
rpoB 761148 c.1342_1344delCGAinsGT frameshift_variant&missense_variant 0.85 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.96 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
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 7832 c.531G>T synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 7835 c.534A>G synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7841 c.540C>T synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7847 c.546G>C synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 7859 c.558A>C synonymous_variant 0.2 levofloxacin
moxifloxacin
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 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 762167 c.2361T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762362 p.Glu852Asp missense_variant 0.23 rifampicin
rpoB 762369 c.2563T>C synonymous_variant 0.23 rifampicin
rpoC 762374 c.-996G>C upstream_gene_variant 0.26 rifampicin
rpoC 762395 c.-975G>C upstream_gene_variant 0.21 rifampicin
rpoC 762398 c.-972T>C upstream_gene_variant 0.21 rifampicin
rpoC 762401 c.-969G>C upstream_gene_variant 0.22 rifampicin
rpoB 762404 c.2598T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 762410 c.-960T>C upstream_gene_variant 0.22 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 762434 c.-936T>C upstream_gene_variant 0.19 rifampicin
rpoC 762443 c.-927G>C upstream_gene_variant 0.2 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762452 c.2646G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763115 c.3309T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763142 c.-228C>G upstream_gene_variant 0.24 rifampicin
rpoC 763160 c.-210G>T upstream_gene_variant 0.32 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763169 c.-201A>G upstream_gene_variant 0.29 rifampicin
rpoC 764485 c.1116G>C synonymous_variant 0.43 rifampicin
rpoC 764491 c.1122G>T synonymous_variant 0.39 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764500 c.1131C>G synonymous_variant 0.35 rifampicin
rpoC 764512 c.1143G>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764605 c.1236G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764623 c.1254C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765121 c.1752G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 766942 c.3573C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766945 c.3576A>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766948 c.3579G>C synonymous_variant 0.19 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304443 p.Ala505Thr missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1407375 c.-36delC upstream_gene_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rpsA 1833829 c.288A>G synonymous_variant 0.19 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.18 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.18 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.15 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.15 pyrazinamide
rpsA 1833904 c.363G>A synonymous_variant 0.13 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.19 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833970 c.429G>T synonymous_variant 0.15 pyrazinamide
rpsA 1833976 c.435C>T synonymous_variant 0.15 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833991 c.450C>A synonymous_variant 0.22 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.23 pyrazinamide
rpsA 1834012 c.471G>T synonymous_variant 0.23 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.23 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.21 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834252 c.711C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834279 c.738C>T synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1834297 c.756C>T synonymous_variant 0.26 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.24 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834345 c.804C>T synonymous_variant 0.27 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
rpsA 1834361 c.820T>C synonymous_variant 0.3 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
rpsA 1834411 c.870T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834423 c.882G>T synonymous_variant 0.24 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.23 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.21 pyrazinamide
rpsA 1834520 p.Ala327Ser missense_variant 0.25 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834543 c.1002C>G synonymous_variant 0.21 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.23 pyrazinamide
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 2155506 c.606C>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170065 p.Ala183Glu missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518085 c.-30C>A upstream_gene_variant 1.0 isoniazid
folC 2747660 c.-62G>C upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv2477c 2783790 p.Val85Ile missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
thyA 3073822 p.Arg217Gln 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
mtrA 3627041 c.307_309delATCinsGG frameshift_variant&missense_variant 0.19 bedaquiline
rifampicin
mtrB 3627044 c.-431C>T upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrB 3627059 c.-446G>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3627062 c.-449G>A upstream_gene_variant 0.18 bedaquiline
rifampicin
rpoA 3877728 c.780C>G synonymous_variant 0.16 rifampicin
rpoA 3877731 c.777G>T synonymous_variant 0.16 rifampicin
rpoA 3877734 c.774G>C synonymous_variant 0.17 rifampicin
rpoA 3877737 c.771G>C synonymous_variant 0.16 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877749 c.759C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
clpC1 4038596 c.2109A>G synonymous_variant 0.23 pyrazinamide
clpC1 4038602 c.2103G>C synonymous_variant 0.22 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.24 pyrazinamide
clpC1 4040841 c.-138delG upstream_gene_variant 1.0 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246088 c.2856A>G synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R