TB-Profiler result

Run: SRR14802041
Summary

Run ID: SRR14802041

Sample name:

Date: 03-04-2023 12:12:36

Number of reads: 5442418

Percentage reads mapped: 99.52

Strain: lineage4.3.3;lineage4.2.1

Drug-resistance: Pre-XDR-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
lineage4.2 Euro-American H;T;LAM None 0.91
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.91
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.06
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
gyrB 6736 p.Asn499Lys missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rpsL 781822 p.Lys88Met missense_variant 0.89 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
pncA 2288848 p.Gly132Ser missense_variant 0.89 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.93 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.93
mshA 576108 p.Ala254Gly missense_variant 0.25
ccsA 619969 p.Val27Ile missense_variant 0.92
rpoC 766467 p.Glu1033Val missense_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074194 p.Ile93Thr missense_variant 0.91
ald 3086742 c.-78A>C upstream_gene_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878580 c.-74_-73insCA upstream_gene_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248324 p.Ala604Gly missense_variant 0.21
embB 4249594 c.3081G>A synonymous_variant 0.89
ethA 4328376 c.-903G>C upstream_gene_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0