TB-Profiler result

Run: ERR11043525
Summary

Run ID: ERR11043525

Sample name:

Date: 31-03-2023 11:36:04

Number of reads: 1110217

Percentage reads mapped: 99.77

Strain: lineage4.4.1.1

Drug-resistance: MDR-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 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
rpoB 761111 p.Asp435Glu missense_variant 1.0 rifampicin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289192 p.Gly17Asp missense_variant 1.0 pyrazinamide
gid 4407796 p.Ser136* stop_gained 1.0 streptomycin
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
ccsA 619785 c.-106G>C upstream_gene_variant 1.0
mmpL5 775626 p.Trp952Leu 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 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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 1.0
alr 3841608 c.-188A>G upstream_gene_variant 1.0
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 1.0
rpoA 3878706 c.-199G>C upstream_gene_variant 0.18
clpC1 4040522 c.183T>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247717 p.Leu402Val missense_variant 1.0
aftB 4268041 c.796C>T synonymous_variant 1.0
ubiA 4269309 p.Trp175Cys missense_variant 0.99
ethA 4326019 c.1455C>T synonymous_variant 1.0
ethA 4326267 p.Cys403Arg missense_variant 1.0
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0
ald 3087391 c.573_*963del frameshift_variant&stop_lost&splice_region_variant 1.0