TB-Profiler result

Run: SRR1173071
Summary

Run ID: SRR1173071

Sample name:

Date: 03-04-2023 03:15:53

Number of reads: 279283

Percentage reads mapped: 95.89

Strain: lineage4.3

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
lineage4.3 Euro-American (LAM) mainly-LAM 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.Ser450Trp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
pncA 2288949 c.-606_292del frameshift_variant&start_lost 1.0 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
gyrB 7121 p.Pro628Thr missense_variant 0.25
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
mshA 576449 p.Pro368Ala missense_variant 0.22
rpoB 761032 p.Gln409Arg missense_variant 0.67
rpoB 761467 p.Leu554Pro missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778272 p.Pro70Gln missense_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303846 p.Phe306Val missense_variant 0.2
fbiC 1303854 c.924T>C synonymous_variant 0.2
fbiC 1303860 c.930A>C synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474710 n.1053T>A non_coding_transcript_exon_variant 0.25
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.2
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.25
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.33
rrl 1476006 n.2349G>A non_coding_transcript_exon_variant 0.2
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155122 p.Asn330Lys missense_variant 0.25
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240200 p.Ala113Glu missense_variant 0.22
embC 4242114 p.Leu751Pro missense_variant 0.2
embC 4242159 p.Leu766Pro missense_variant 0.25
embA 4242313 c.-920C>A upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242654 p.Ala931Gly missense_variant 0.4
embB 4248238 p.Met575Ile missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0