TB-Profiler result

Run: SRR1196534
Summary

Run ID: SRR1196534

Sample name:

Date: 03-04-2023 05:28:25

Number of reads: 1033133

Percentage reads mapped: 97.82

Strain: lineage4.3.3

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
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
rpoB 761155 p.Ser450Trp missense_variant 0.96 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
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
rpoB 761032 p.Gln409Arg missense_variant 1.0
rpoB 761467 p.Leu554Pro missense_variant 1.0
rpoB 763246 c.3442delG frameshift_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765545 p.Arg726Cys missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778142 c.-848G>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801235 p.Ala143Ser missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
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
pepQ 2860469 c.-51C>T upstream_gene_variant 0.12
Rv2752c 3064817 p.Asp459Asn missense_variant 0.12
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
Rv3083 3449126 p.Thr208Lys missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239863 c.1A>G start_lost 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
pncA 2288947 c.-606_294del start_lost&conservative_inframe_deletion 1.0
gid 4407912 c.160_290del frameshift_variant 1.0