TB-Profiler result

Run: ERR4800060
Summary

Run ID: ERR4800060

Sample name:

Date: 01-04-2023 09:34:01

Number of reads: 3389472

Percentage reads mapped: 99.55

Strain: lineage4.1.2.1

Drug-resistance: 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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.97 linezolid
fabG1 1673432 c.-8T>A upstream_gene_variant 0.98 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289216 p.Val9Gly missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.99 kanamycin
embB 4247431 p.Met306Ile 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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.98
mshA 575679 p.Asn111Ser missense_variant 0.98
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764585 p.Leu406Phe missense_variant 0.99
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417213 p.Asn45Lys missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475927 n.2270G>T non_coding_transcript_exon_variant 1.0
rpsA 1834919 c.1379dupC frameshift_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746923 p.Gly226Arg missense_variant 0.99
folC 2747481 p.Glu40Lys missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
alr 3840259 p.Tyr388Asp missense_variant 0.98
alr 3841546 c.-126C>A upstream_gene_variant 0.97
alr 3841568 c.-148G>A upstream_gene_variant 0.9
alr 3841570 c.-151delA upstream_gene_variant 0.9
alr 3841574 c.-154T>G upstream_gene_variant 0.9
alr 3841578 c.-158G>T upstream_gene_variant 0.9
alr 3841582 c.-162A>G upstream_gene_variant 0.9
alr 3841584 c.-164C>A upstream_gene_variant 0.9
alr 3841589 c.-170delG upstream_gene_variant 0.95
alr 3841612 c.-193_-192insC upstream_gene_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4326339 p.Asn379His missense_variant 0.99
whiB6 4338426 c.96C>T synonymous_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0