TB-Profiler result

Run: SRR14807625
Summary

Run ID: SRR14807625

Sample name:

Date: 03-04-2023 12:29:54

Number of reads: 1929958

Percentage reads mapped: 99.65

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.51
lineage4.2 Euro-American H;T;LAM None 0.47
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.46
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.54
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.Asp94Ala missense_variant 0.57 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.6 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.55 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.45 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.46 pyrazinamide
pncA 2289234 c.7delG frameshift_variant 0.57 pyrazinamide, pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.48 kanamycin
eis 2715344 c.-12C>T upstream_gene_variant 0.56 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.51 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.47 ethambutol
ethA 4326942 c.531dupC frameshift_variant 0.55 ethionamide, 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 0.57
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.49
mshA 576108 p.Ala254Gly missense_variant 0.3
ccsA 619969 p.Val27Ile missense_variant 0.58
rpoB 759862 p.Gln19Arg missense_variant 0.6
rpoC 764817 p.Val483Gly missense_variant 0.43
rpoC 764995 c.1626C>G synonymous_variant 0.49
mmpL5 775639 p.Ile948Val missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.55
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.66
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.51
PPE35 2169879 p.Phe245Cys missense_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.41
folC 2746340 p.Ala420Val missense_variant 0.43
Rv2752c 3066102 p.Asn30Lys missense_variant 0.66
thyA 3073868 p.Thr202Ala missense_variant 0.57
ald 3086742 c.-78A>C upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.3
clpC1 4038287 c.2418C>T synonymous_variant 0.43
clpC1 4038968 c.1737G>A synonymous_variant 0.6
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 0.38
ubiA 4269124 p.Ala237Val missense_variant 0.4
ethA 4326467 p.Asp336Gly missense_variant 0.48
ethA 4326632 p.His281Pro missense_variant 0.46
ethA 4328376 c.-903G>C upstream_gene_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.6