TB-Profiler result

Run: SRR10851704
Summary

Run ID: SRR10851704

Sample name:

Date: 02-04-2023 19:32:36

Number of reads: 1365375

Percentage reads mapped: 81.54

Strain: lineage4.1.2;lineage4.1.1.3

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 0.14
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.86
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.89
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 6579 p.Ser447Phe missense_variant 0.83 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rpoC 764724 p.Phe452Ser missense_variant 0.91 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.93 streptomycin
katG 2155167 p.Ser315Thr missense_variant 0.75 isoniazid
pncA 2288827 p.Val139Met missense_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.89 isoniazid
embB 4247429 p.Met306Val missense_variant 0.88 ethambutol
ethA 4326876 c.597delC frameshift_variant 0.86 ethionamide, ethionamide
ethR 4327876 p.Phe110Leu missense_variant 0.2 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
gyrB 6608 p.Val457Leu missense_variant 0.86
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.35
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 0.15
rplC 801354 c.546G>A synonymous_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.98
PPE35 2168303 c.2310G>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449616 p.Met371Ile missense_variant 0.84
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840263 c.1158C>T synonymous_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.15
embB 4249408 c.2895G>A synonymous_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0