TB-Profiler result

Run: ERR4813321
Summary

Run ID: ERR4813321

Sample name:

Date: 01-04-2023 12:40:30

Number of reads: 225708

Percentage reads mapped: 99.51

Strain: lineage4

Drug-resistance: MDR-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
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Thr missense_variant 0.56 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289097 p.Asp49Asn missense_variant 0.5 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326716 c.757delT frameshift_variant 0.75 ethionamide, ethionamide
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 6107 p.Ala290Thr missense_variant 0.29
gyrB 6836 p.Ala533Pro missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.62
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761880 p.Ala692Thr missense_variant 1.0
rpoB 762288 p.Asp828Tyr missense_variant 0.13
rpoC 764817 p.Val483Gly missense_variant 0.86
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765804 p.Thr812Ile missense_variant 0.5
rpoC 766414 p.Phe1015Leu missense_variant 0.4
rpoC 766453 c.3084G>A synonymous_variant 0.22
rpoC 766482 p.Arg1038Leu missense_variant 0.22
rpoC 766537 p.Glu1056Asp missense_variant 0.17
mmpL5 777278 c.1203G>A synonymous_variant 0.67
mmpL5 778414 p.Phe23Leu missense_variant 0.25
mmpL5 778979 c.-499G>A upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303060 p.Ala44Ser missense_variant 0.5
embR 1416513 p.Gln279Lys missense_variant 0.25
embR 1416517 c.831C>A synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
katG 2154459 c.1653C>T synonymous_variant 0.71
katG 2155017 c.1095G>A synonymous_variant 0.55
Rv1979c 2222523 c.642C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.67
folC 2747453 p.Arg49Gln missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449896 p.His465Asn missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474297 p.Tyr97* stop_gained 0.14
Rv3236c 3612230 p.Ala296Val missense_variant 0.4
fbiB 3642618 p.Asp362Asn missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
ethA 4327197 p.Gly93* stop_gained 0.25
ethA 4327527 c.-54G>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 0.38
gid 4407720 c.483C>G synonymous_variant 0.55
gid 4408003 p.Asp67Gly missense_variant 0.86
gid 4408156 p.Leu16Arg missense_variant 1.0