TB-Profiler result

Run: ERR2653198
Summary

Run ID: ERR2653198

Sample name:

Date: 31-03-2023 22:39:44

Number of reads: 8929288

Percentage reads mapped: 97.43

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.98
lineage4.4.1 Euro-American (S-type) S;T None 0.97
lineage4.4.1.1 Euro-American S;Orphans None 0.98
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 6735 p.Asn499Thr missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289015 p.Thr76Ile missense_variant 0.97 pyrazinamide
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760315 p.Val170Ala missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304085 c.1155C>T synonymous_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 0.98
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
pepQ 2859680 c.739C>T synonymous_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.98
fbiB 3640905 c.-630C>T upstream_gene_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.99
embB 4248084 p.Arg524His missense_variant 0.96
ethA 4326442 p.Leu344Phe missense_variant 0.98
ethA 4327063 p.Cys137Trp missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407839 c.363dupG frameshift_variant 0.99