TB-Profiler result

Run: ERR5530521

Summary

Run ID: ERR5530521

Sample name:

Date: 01-04-2023 22:33:38

Number of reads: 4776901

Percentage reads mapped: 99.71

Strain: lineage4.3.4.1

Drug-resistance: Pre-XDR-TB


Download CSV Download TXT Download PDF Download JSON
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 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 1.0
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289067 p.Ser59Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 1.0 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
gyrA 9315 c.2014C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.23
mshA 576613 c.1266A>C synonymous_variant 0.31
mshA 576616 c.1269G>C synonymous_variant 0.22
rpoB 762793 p.Val996Ala missense_variant 0.13
rpoC 764367 p.Gly333Ala missense_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767123 p.Val1252Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102307 p.Gly246Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.25
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.21
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.53
fbiD 3339751 p.Ala212Pro missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.21
embB 4247723 p.Pro404Ala missense_variant 1.0
embB 4248328 c.1815G>C synonymous_variant 0.23
whiB6 4338440 c.81dupT frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0