TB-Profiler result

Run: ERR4821179
Summary

Run ID: ERR4821179

Sample name:

Date: 2024-04-16T07:24:46.985662

Number of reads: 3409122

Percentage reads mapped: 89.99

Median coverage: 67.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.99
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American 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
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.888G>A Uncertain significance Mutation from literature
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance Mutation from literature
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 7216 c.1977G>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7225 c.-77T>C upstream_gene_variant 0.12 levofloxacin
moxifloxacin
gyrA 7237 c.-65C>T upstream_gene_variant 0.12 levofloxacin
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 7715 c.414G>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8603 c.1302A>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8624 c.1323G>C synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8627 c.1326C>G synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8636 c.1335A>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 656578 p.Cys298Phe missense_variant 0.97 ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 0.94 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.92 rifampicin Not assoc w R
rpoB 761531 c.1725C>G synonymous_variant 0.12 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762266 c.2460T>C synonymous_variant 0.13 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.13 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763028 c.3222T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.15 rifampicin
rpoC 763717 c.348T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.14 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.15 rifampicin
rpoC 763735 c.366G>C synonymous_variant 0.14 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.13 rifampicin
rpoC 763996 c.627T>C synonymous_variant 0.17 rifampicin
rpoC 764005 c.636G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764011 c.642T>C synonymous_variant 0.17 rifampicin
rpoC 764040 p.Ser224Asn missense_variant 0.14 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.14 rifampicin
rpoC 764116 c.747C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.12 rifampicin
rpoC 764824 c.1455T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764830 c.1461C>G synonymous_variant 0.13 rifampicin
rpoC 764872 c.1503A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.13 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.13 rifampicin
rpoC 764932 c.1563C>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 766864 c.3495G>C synonymous_variant 0.13 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1304808 c.1878C>G synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1304811 c.1881C>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304817 c.1887T>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1304829 c.1899T>C synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1304832 c.1902C>G synonymous_variant 0.23 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.96 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.64 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.9 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 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674537 c.336C>G synonymous_variant 0.17 ethionamide
isoniazid
inhA 1674542 p.Ala114Glu missense_variant 0.16 ethionamide
isoniazid
inhA 1674549 c.348G>C synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674561 c.360C>T synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674582 c.381T>C synonymous_variant 0.18 ethionamide
isoniazid
inhA 1674585 c.384T>C synonymous_variant 0.19 ethionamide
isoniazid
inhA 1674589 p.Met130Leu missense_variant 0.19 ethionamide
isoniazid
inhA 1674624 c.423A>C synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674627 c.426T>C synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674630 c.429C>G synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674636 c.435C>G synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674654 c.453G>C synonymous_variant 0.14 ethionamide
isoniazid
rpsA 1833554 p.Thr5Ala missense_variant 0.18 pyrazinamide Uncertain significance
rpsA 1833568 c.27G>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1833589 c.48A>T synonymous_variant 0.17 pyrazinamide
rpsA 1833595 c.54T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833619 c.78A>C synonymous_variant 0.17 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833790 c.249T>A synonymous_variant 0.16 pyrazinamide
rpsA 1833799 c.258C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.21 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.21 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.21 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.25 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.24 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.31 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834261 c.720A>C synonymous_variant 0.13 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.13 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 2155032 c.1080T>C synonymous_variant 0.13 isoniazid Not assoc w R - Interim
katG 2155054 p.Tyr353Phe missense_variant 0.15 isoniazid
katG 2155056 c.1056A>G synonymous_variant 0.15 isoniazid
katG 2155062 c.1050T>C synonymous_variant 0.16 isoniazid
katG 2155065 c.1047C>G synonymous_variant 0.17 isoniazid
katG 2155068 c.1044T>C synonymous_variant 0.16 isoniazid
katG 2155071 c.1041T>C synonymous_variant 0.16 isoniazid
katG 2155080 c.1032G>C synonymous_variant 0.17 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.15 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.19 capreomycin
thyA 3073953 c.519T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073977 c.495A>G synonymous_variant 0.15 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
rpoA 3877587 c.921A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878143 p.Gly122Asp missense_variant 0.11 rifampicin Uncertain significance
clpC1 4038530 p.Glu725Asp missense_variant 0.13 pyrazinamide
clpC1 4038536 c.2169C>T synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.2 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039187 c.1518G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039190 c.1515C>G synonymous_variant 0.12 pyrazinamide
clpC1 4039208 c.1497C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039226 c.1479T>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
clpC1 4039268 c.1437C>G synonymous_variant 0.29 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
clpC1 4039286 c.1419T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039289 c.1416T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039295 c.1410A>C synonymous_variant 0.2 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.22 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039322 c.1383T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039493 c.1212C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039517 c.1188C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039524 p.Phe394Tyr missense_variant 0.17 pyrazinamide
clpC1 4039526 c.1179G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039532 c.1173C>T synonymous_variant 0.15 pyrazinamide
clpC1 4039586 c.1119G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.2 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.22 pyrazinamide
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.21 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.18 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039979 c.726C>G synonymous_variant 0.13 pyrazinamide
clpC1 4040465 c.240T>C synonymous_variant 0.14 pyrazinamide
clpC1 4040471 c.234T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4040477 c.228G>A synonymous_variant 0.18 pyrazinamide
clpC1 4040480 c.225T>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4040522 c.183T>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
glpK 4138268 c.1488T>C synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4240561 c.699C>G synonymous_variant 0.12 ethambutol
embC 4240578 p.Ala239Val missense_variant 0.13 ethambutol
embC 4240582 c.720C>G synonymous_variant 0.13 ethambutol
embC 4240591 c.729C>G synonymous_variant 0.13 ethambutol
embC 4242643 c.2781C>T synonymous_variant 0.98 ethambutol Not assoc w R
embC 4242803 p.Val981Leu 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 0.98 capreomycin
amikacin
kanamycin