TB-Profiler result

Run: ERR2653213
Summary

Run ID: ERR2653213

Sample name:

Date: 31-03-2023 22:40:21

Number of reads: 3488206

Percentage reads mapped: 98.5

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.98
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
gyrA 7582 p.Asp94Gly missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.98 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
rpoB 762027 p.Leu741Phe missense_variant 0.98
rpoB 762310 p.His835Pro missense_variant 0.98
rpoC 765150 p.Gly594Glu missense_variant 0.97
rpoC 765730 c.2361G>A synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781767 p.Glu70Lys missense_variant 0.97
rplC 801115 p.Ala103Thr missense_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167931 c.2682C>T synonymous_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087647 c.830dupG frameshift_variant 0.63
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 0.99
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878599 c.-92C>G upstream_gene_variant 0.13
rpoA 3878601 c.-95delG upstream_gene_variant 0.16
embC 4240897 c.1035C>G synonymous_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.97
embB 4249408 c.2895G>A synonymous_variant 0.96
ethA 4327331 p.Phe48Ser missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0