TB-Profiler result

Run: SRR1169241
Summary

Run ID: SRR1169241

Sample name:

Date: 03-04-2023 02:50:00

Number of reads: 848352

Percentage reads mapped: 97.22

Strain: lineage4.1.1.3

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 1.0 pyrazinamide
ald 3087278 c.464delG frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 1.0 ethionamide
ethA 4326604 c.869dupA 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
gyrB 5112 c.-128G>T upstream_gene_variant 0.12
gyrB 7107 p.Glu623Gly missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575726 p.Thr127Ser missense_variant 0.17
rpoB 762252 p.Arg816Ser missense_variant 0.12
rpoB 762285 p.Arg827Cys missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765253 c.1886_1887delTG frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777411 p.Ile357Thr missense_variant 0.13
mmpS5 778593 c.312delC frameshift_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.1
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.1
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.13
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.14
rpsA 1833413 c.-129G>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917975 c.36C>A synonymous_variant 0.14
ndh 2102627 p.Lys139Arg missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289704 c.-463G>T upstream_gene_variant 0.14
thyA 3074341 p.Leu44Pro missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
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 4249408 c.2895G>A synonymous_variant 0.95
aftB 4267329 p.Arg503Leu missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0