TB-Profiler result

Run: SRR14801928
Summary

Run ID: SRR14801928

Sample name:

Date: 03-04-2023 12:08:06

Number of reads: 1704754

Percentage reads mapped: 99.63

Strain: lineage4.3.3;lineage4.2.1

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 0.21
lineage4.2 Euro-American H;T;LAM None 0.81
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.8
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.2
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 0.85 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.72 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.8 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.88 isoniazid
pncA 2289119 c.110_122delAAGCGGCGGACTA frameshift_variant 0.86 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.79 kanamycin
embB 4248003 p.Gln497Arg missense_variant 0.8 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 8040 p.Gly247Ser missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.8
ccsA 619969 p.Val27Ile missense_variant 0.86
rpoB 762391 p.Leu862Arg missense_variant 0.83
rpoC 764995 c.1626C>G synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.73
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.19
thyA 3073868 p.Thr202Ala missense_variant 0.13
ald 3086742 c.-78A>C upstream_gene_variant 0.77
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 0.14
embA 4242571 c.-662C>T upstream_gene_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.19
embB 4249594 c.3081G>A synonymous_variant 0.81
ubiA 4269293 p.Ala181Thr missense_variant 0.75
ethA 4326632 p.His281Pro missense_variant 0.85
ethA 4328376 c.-903G>C upstream_gene_variant 0.76
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.28