TB-Profiler result

Run: ERR4821330
Summary

Run ID: ERR4821330

Sample name:

Date: 01-04-2023 17:11:37

Number of reads: 641514

Percentage reads mapped: 99.72

Strain: lineage4.6.2.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 1.0
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247652 p.Ser380Asn missense_variant 0.2 ethambutol
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
gyrB 5128 c.-112T>C upstream_gene_variant 0.22
gyrB 6402 p.Cys388Ser missense_variant 0.13
gyrB 6494 p.Ala419Thr missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7803 p.Ser168Arg missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491063 p.Gly94Glu missense_variant 0.18
mshA 576053 p.Asp236Asn missense_variant 0.13
rpoB 760768 p.Pro321Leu missense_variant 0.13
rpoC 763418 p.Ala17Thr missense_variant 0.13
rpoC 766651 c.3282T>A synonymous_variant 0.2
rpoC 766915 p.Asp1182Glu missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
mmpL5 778428 p.His18Arg missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416766 c.582C>A synonymous_variant 0.13
embR 1416827 p.His174Arg missense_variant 0.14
atpE 1461216 p.Gly58Cys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
fabG1 1673722 p.Ala95Thr missense_variant 0.15
rpsA 1833546 p.Pro2Leu missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154315 c.1797A>T synonymous_variant 0.11
katG 2155179 c.933C>T synonymous_variant 0.12
katG 2155389 c.723C>G synonymous_variant 1.0
katG 2155727 p.Phe129Leu missense_variant 0.22
PPE35 2168509 p.Val702Phe missense_variant 0.12
PPE35 2170556 c.57G>A synonymous_variant 0.12
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2222319 c.846C>T synonymous_variant 0.15
Rv1979c 2222882 p.Gly95Cys missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289433 c.-192C>A upstream_gene_variant 0.13
folC 2746279 c.1320C>T synonymous_variant 0.17
Rv2752c 3065360 p.Phe278Leu missense_variant 0.22
Rv2752c 3065522 c.670C>A synonymous_variant 0.2
Rv2752c 3066089 p.Glu35* stop_gained 0.14
thyX 3067307 c.639C>T synonymous_variant 0.14
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyX 3067483 p.Ala155Ser missense_variant 0.15
thyX 3067712 c.234G>A synonymous_variant 0.22
ald 3087255 p.Ala146Pro missense_variant 0.2
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
alr 3840308 c.1113G>A synonymous_variant 0.11
clpC1 4040144 c.561G>C synonymous_variant 0.18
embC 4242330 p.Glu823Ala missense_variant 0.12
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243563 c.332delA frameshift_variant 0.11
embB 4246981 c.468C>A synonymous_variant 0.13
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4326983 p.Pro164Leu missense_variant 0.2
ethR 4327198 c.-351A>G upstream_gene_variant 0.17
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0