TB-Profiler result

Run: ERR987751
Summary

Run ID: ERR987751

Sample name:

Date: 02-04-2023 13:23:08

Number of reads: 1506929

Percentage reads mapped: 99.64

Strain: lineage4.6.1.2;lineage4.2.2.2

Drug-resistance: MDR-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
lineage4.6 Euro-American T;LAM None 0.76
lineage4.2 Euro-American H;T;LAM None 0.19
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.19
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.79
lineage4.6.1.2 Euro-American T2 RD724 0.81
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.18
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 761139 p.His445Tyr missense_variant 0.17 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.65 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7539 p.Thr80Ala missense_variant 0.86
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.21
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.17
rpoB 761489 c.1683G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776450 c.2031C>A synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781676 c.117C>T synonymous_variant 0.69
embR 1416410 p.Leu313Arg missense_variant 0.81
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673152 c.-288A>G upstream_gene_variant 0.81
inhA 1674465 c.264C>T synonymous_variant 0.78
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918405 p.Ser156Pro missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518586 p.Leu158Phe missense_variant 0.76
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.12
ald 3086742 c.-78A>C upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641586 p.Ile18Val missense_variant 0.69
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.75
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 0.89
gid 4408061 p.His48Asn missense_variant 0.29