TB-Profiler result

Run: ERR4827458
Summary

Run ID: ERR4827458

Sample name:

Date: 01-04-2023 18:03:56

Number of reads: 1156786

Percentage reads mapped: 99.43

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 0.11 pyrazinamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619815 c.-76G>C upstream_gene_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766667 p.Ser1100Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775681 p.Gly934Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406998 p.Ala115Thr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101684 p.Gln453His missense_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2169293 c.1320T>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.52
PPE35 2170147 p.Ser156Ala missense_variant 0.19
PPE35 2170159 p.Ala152Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746538 p.His354Leu missense_variant 0.13
folC 2747273 p.Ser109* stop_gained 0.18
pepQ 2860144 p.Val92Gly missense_variant 0.23
Rv2752c 3065533 p.Pro220Leu missense_variant 0.12
thyX 3067286 c.660C>A synonymous_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339490 p.Leu125Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474640 c.634T>C synonymous_variant 0.13
fprA 3475000 p.Leu332Met missense_variant 0.2
fbiB 3642774 p.Leu414Met missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241663 p.Gly601Arg missense_variant 0.67
embC 4242526 c.2667delG frameshift_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243372 p.Gln47Arg missense_variant 0.18
embA 4244823 p.Val531Leu missense_variant 1.0
embA 4245820 p.Ser863Ile missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4248316 c.1803C>T synonymous_variant 1.0
embB 4249199 p.Gln896Glu missense_variant 0.11
ethA 4328459 c.-986A>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Ala missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0