TB-Profiler result

Run: ERR6865775
Summary

Run ID: ERR6865775

Sample name:

Date: 02-04-2023 03:05:01

Number of reads: 1652788

Percentage reads mapped: 99.51

Strain: lineage4.1.2.1;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 1.0
lineage4.1.2 Euro-American T;H None 0.29
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.76
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.27
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 7572 p.Ser91Pro missense_variant 0.75 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Phe missense_variant 0.83 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.76 isoniazid, ethionamide
katG 2155168 p.Ser315Asn missense_variant 0.8 isoniazid
pncA 2289231 p.Leu4Trp missense_variant 0.7 pyrazinamide
embB 4248002 p.Gln497Lys missense_variant 0.79 ethambutol
gid 4407618 p.Tyr195* stop_gained 0.8 streptomycin
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 5133 c.-107A>C upstream_gene_variant 0.71
gyrB 6052 p.Ile271Met missense_variant 0.8
gyrB 7221 p.Ser661Thr missense_variant 0.84
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.98
gyrA 9620 c.2319G>A synonymous_variant 0.35
fgd1 491591 p.Lys270Met missense_variant 0.25
mshA 575679 p.Asn111Ser missense_variant 0.24
rpoB 760115 c.309C>T synonymous_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765669 p.His767Pro missense_variant 0.77
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 0.8
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673865 c.-337C>T upstream_gene_variant 0.78
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.23
Rv2752c 3065797 p.Gln132Pro missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087605 c.786G>T synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 0.73
ubiA 4269298 p.Ile179Thr missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408159 p.Arg15Pro missense_variant 0.29