TB-Profiler result

Run: SRR6831950
Summary

Run ID: SRR6831950

Sample name:

Date: 2024-10-04T15:32:30.726482

Number of reads: 2394279

Percentage reads mapped: 89.65

Median coverage: 48.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.99
lineage4 Euro-American None 0.99
lineage4.3.3 Euro-American (LAM) RD115 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
dnaA 805 c.805T>C synonymous_variant 0.17 isoniazid
dnaA 813 c.813C>T synonymous_variant 0.17 isoniazid
dnaA 822 c.822A>G synonymous_variant 0.17 isoniazid
dnaA 828 c.828T>C synonymous_variant 0.17 isoniazid Not assoc w R - Interim
dnaA 831 c.831A>G synonymous_variant 0.17 isoniazid
dnaA 837 c.837A>G synonymous_variant 0.18 isoniazid
dnaA 840 c.840G>A synonymous_variant 0.19 isoniazid
dnaA 843 c.843T>C synonymous_variant 0.19 isoniazid Not assoc w R - Interim
dnaA 846 c.846T>C synonymous_variant 0.19 isoniazid
dnaA 849 c.849A>G synonymous_variant 0.18 isoniazid
dnaA 885 c.885T>C synonymous_variant 0.18 isoniazid
dnaA 1104 c.1104T>C synonymous_variant 0.14 isoniazid
dnaA 1110 c.1110T>C synonymous_variant 0.14 isoniazid
dnaA 1122 c.1122C>A synonymous_variant 0.14 isoniazid Not assoc w R - Interim
dnaA 1125 c.1125G>C synonymous_variant 0.15 isoniazid
dnaA 1152 c.1152A>G synonymous_variant 0.15 isoniazid
dnaA 1153 c.1153T>C synonymous_variant 0.15 isoniazid
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 8040 p.Gly247Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8366 c.1065G>C synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 8375 c.1074G>C synonymous_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8391 p.Tyr364His missense_variant 0.3 levofloxacin
moxifloxacin
gyrA 8399 c.1098T>C synonymous_variant 0.31 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8420 c.1119T>C synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 8423 c.1122G>C synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 8442 c.1141C>T synonymous_variant 0.34 levofloxacin
moxifloxacin
gyrA 8453 c.1152A>C synonymous_variant 0.37 levofloxacin
moxifloxacin
gyrA 8504 c.1203G>C synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 8516 c.1215T>C synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 8519 c.1218A>C synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 8537 c.1236G>A synonymous_variant 0.3 levofloxacin
moxifloxacin
gyrA 8546 c.1245T>C synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8552 c.1251C>G synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 8556 p.Ala419Gln missense_variant 0.28 levofloxacin
moxifloxacin
gyrA 8561 c.1260A>C synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8562 c.1261C>T synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8576 c.1275C>G synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 8998 p.Leu566Trp missense_variant 0.18 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
hadA 731741 c.-189G>A upstream_gene_variant 0.2 isoniazid
hadA 731747 c.-183T>C upstream_gene_variant 0.21 isoniazid
hadA 731753 c.-177A>G upstream_gene_variant 0.23 isoniazid
hadA 731774 c.-156T>C upstream_gene_variant 0.22 isoniazid
hadA 731789 c.-141A>G upstream_gene_variant 0.23 isoniazid
hadA 731792 c.-138G>A upstream_gene_variant 0.23 isoniazid
hadA 731801 c.-129C>G upstream_gene_variant 0.21 isoniazid
hadA 731816 c.-114G>A upstream_gene_variant 0.17 isoniazid
nusG 734457 c.204C>G synonymous_variant 0.15 rifampicin
nusG 734472 c.219T>C synonymous_variant 0.15 rifampicin
nusG 734475 c.222T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734481 c.228C>G synonymous_variant 0.16 rifampicin
nusG 734499 c.246G>C synonymous_variant 0.13 rifampicin
rpoB 760886 c.1080A>G synonymous_variant 0.21 rifampicin
rpoB 760919 c.1113C>G synonymous_variant 0.2 rifampicin
rpoB 760925 c.1119T>C synonymous_variant 0.21 rifampicin
rpoB 760928 c.1122G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760934 c.1128C>T synonymous_variant 0.19 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763028 c.3222T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.27 rifampicin
rpoB 763085 c.3279C>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.19 rifampicin
rpoC 763158 c.-212C>T upstream_gene_variant 0.16 rifampicin
rpoC 763402 c.33C>G synonymous_variant 0.25 rifampicin
rpoC 763411 c.42T>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 763414 c.45T>C synonymous_variant 0.27 rifampicin
rpoC 763441 c.72C>G synonymous_variant 0.32 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763708 c.339G>A synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763709 c.340C>T synonymous_variant 0.23 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.3 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.37 rifampicin
rpoC 763735 c.366G>C synonymous_variant 0.35 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.35 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.37 rifampicin
rpoC 763768 c.399C>G synonymous_variant 0.35 rifampicin
rpoC 763780 c.411C>G synonymous_variant 0.31 rifampicin
rpoC 763783 c.414G>C synonymous_variant 0.29 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.21 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764188 c.819A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764195 p.Ser276Gln missense_variant 0.16 rifampicin
rpoC 764203 c.834G>T synonymous_variant 0.16 rifampicin
rpoC 764257 c.888G>C synonymous_variant 0.38 rifampicin
rpoC 764893 c.1524T>C synonymous_variant 0.17 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.18 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 765007 c.1638T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765928 c.2559C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765985 c.2616C>T synonymous_variant 0.19 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766726 c.3357T>C synonymous_variant 0.13 rifampicin
rpoC 766738 c.3369G>T synonymous_variant 0.15 rifampicin
mmpL5 775639 p.Ile948Val 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
rpsL 781760 c.201T>C synonymous_variant 0.14 streptomycin
rpsL 781793 c.234G>C synonymous_variant 0.14 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.17 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.2 streptomycin
rpsL 781859 c.300T>C synonymous_variant 0.15 streptomycin Not assoc w R - Interim
rpsL 781868 c.309T>C synonymous_variant 0.16 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.17 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.2 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.21 streptomycin
rplC 800582 c.-227C>G upstream_gene_variant 0.12 linezolid
rplC 800814 c.6A>G synonymous_variant 0.2 linezolid
rplC 800817 c.9A>T synonymous_variant 0.2 linezolid
rplC 800844 c.36T>C synonymous_variant 0.15 linezolid
fbiC 1303095 c.165G>A synonymous_variant 0.96 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
atpE 1461185 c.141G>C synonymous_variant 0.22 bedaquiline
atpE 1461189 c.145C>T synonymous_variant 0.21 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
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 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674315 c.114C>G synonymous_variant 0.26 isoniazid
ethionamide
inhA 1674321 c.120G>C synonymous_variant 0.3 isoniazid
ethionamide
inhA 1674342 c.141T>C synonymous_variant 0.21 isoniazid
ethionamide
inhA 1674537 c.336C>G synonymous_variant 0.21 isoniazid
ethionamide
inhA 1674542 p.Ala114Glu missense_variant 0.22 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 0.21 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 0.19 isoniazid
ethionamide
inhA 1674624 c.423A>C synonymous_variant 0.18 isoniazid
ethionamide
inhA 1674627 c.426T>G synonymous_variant 0.21 isoniazid
ethionamide
inhA 1674630 c.429C>G synonymous_variant 0.21 isoniazid
ethionamide
rpsA 1834836 p.Met432Thr missense_variant 1.0 pyrazinamide Not assoc w R - Interim
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 2156196 c.-85C>T upstream_gene_variant 1.0 isoniazid 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
kasA 2518919 p.Gly269Ser missense_variant 0.94 isoniazid
folC 2746340 p.Ala420Val missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2783365 c.678C>T synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783373 p.Glu224Gln missense_variant 0.26 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783395 c.648T>C synonymous_variant 0.27 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073824 c.648A>C synonymous_variant 0.12 para-aminosalicylic_acid
thyA 3073839 c.633T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073863 c.609T>C synonymous_variant 0.19 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.8 para-aminosalicylic_acid
thyA 3073872 p.Ile200Val missense_variant 0.2 para-aminosalicylic_acid
thyA 3073878 c.594G>A synonymous_variant 0.22 para-aminosalicylic_acid
thyA 3074172 c.300G>C synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3074175 c.297A>G synonymous_variant 0.13 para-aminosalicylic_acid
thyA 3074199 c.273G>A synonymous_variant 0.16 para-aminosalicylic_acid
thyA 3074205 p.Glu89Asp missense_variant 0.17 para-aminosalicylic_acid
thyA 3074214 c.258T>C synonymous_variant 0.17 para-aminosalicylic_acid
thyA 3074217 c.255T>C synonymous_variant 0.21 para-aminosalicylic_acid
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
mtrA 3627242 c.108C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3877692 c.816G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878082 c.426T>C synonymous_variant 0.16 rifampicin
rpoA 3878141 p.Met123Leu missense_variant 0.2 rifampicin Uncertain significance
rpoA 3878142 p.Gly122Glu missense_variant 0.21 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878199 c.309T>C synonymous_variant 0.16 rifampicin
rpoA 3878202 c.306G>C synonymous_variant 0.16 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.15 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.87 pyrazinamide Not assoc w R
clpC1 4038293 c.2412G>C synonymous_variant 0.17 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.23 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.22 pyrazinamide
clpC1 4038815 c.1890G>T synonymous_variant 0.22 pyrazinamide
clpC1 4038968 c.1737G>A synonymous_variant 0.92 pyrazinamide Not assoc w R - Interim
clpC1 4039586 c.1119G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.17 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.17 pyrazinamide
clpC1 4039622 c.1083C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039817 c.888A>T synonymous_variant 0.13 pyrazinamide
clpC1 4039820 c.885T>G synonymous_variant 0.13 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039832 c.873C>G synonymous_variant 0.14 pyrazinamide
clpC1 4040354 c.351A>G synonymous_variant 0.21 pyrazinamide
panD 4045034 c.-753A>T upstream_gene_variant 0.13 pyrazinamide
embC 4241086 c.1224G>C synonymous_variant 0.22 ethambutol
embC 4241104 c.1242G>A synonymous_variant 0.24 ethambutol Not assoc w R - Interim
embC 4241509 c.1647A>G synonymous_variant 1.0 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248064 c.1551G>C synonymous_variant 0.17 ethambutol Not assoc w R - Interim
embB 4248070 c.1557T>C synonymous_variant 0.16 ethambutol
embB 4248085 c.1572T>C synonymous_variant 0.16 ethambutol
embB 4248097 c.1584C>G synonymous_variant 0.14 ethambutol
embB 4248127 c.1614G>C synonymous_variant 0.13 ethambutol
embB 4248133 c.1620C>G synonymous_variant 0.16 ethambutol
embB 4248142 c.1629T>C synonymous_variant 0.16 ethambutol
embB 4248143 c.1630T>C synonymous_variant 0.15 ethambutol
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 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R