TB-Profiler result

Run: ERR6397174
Summary

Run ID: ERR6397174

Sample name:

Date: 02-04-2023 02:45:38

Number of reads: 6446572

Percentage reads mapped: 99.56

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247495 p.Asp328Tyr missense_variant 1.0 ethambutol
ethA 4326066 c.1407delG frameshift_variant 1.0 ethionamide, 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
rpoB 759939 p.Pro45Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776273 c.2199_2207dupGCGCATCGC disruptive_inframe_insertion 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rpsL 781676 c.117C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288967 p.Ala92Val missense_variant 1.0
pncA 2289128 c.114G>C synonymous_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726556 p.Ala122Thr missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.22
fbiD 3339741 c.624G>T synonymous_variant 0.12
fbiD 3339744 c.627A>C synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.27
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.28
embB 4246563 p.Leu17Trp missense_variant 0.24
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4246584 p.Arg24Pro missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0