TB-Profiler result

Run: SRR6896240
Summary

Run ID: SRR6896240

Sample name:

Date: 04-04-2023 17:59:50

Number of reads: 390651

Percentage reads mapped: 99.53

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 0.92 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 7941 p.Glu214Lys missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762285 p.Arg827Cys missense_variant 1.0
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
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473543 n.-115C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168247 p.Leu789His missense_variant 0.22
PPE35 2169144 p.Val490Gly missense_variant 0.12
PPE35 2169148 p.Ala489Thr missense_variant 0.12
Rv1979c 2222994 c.170delT frameshift_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289750 c.-509C>T upstream_gene_variant 0.12
eis 2714708 p.Gly209Cys missense_variant 0.13
Rv2752c 3065145 c.1046delT frameshift_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086882 c.63C>A synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640457 c.-86G>A upstream_gene_variant 0.29
fbiB 3642552 p.Ile340Val missense_variant 0.14
clpC1 4039010 c.1695G>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243525 p.Val98Ala missense_variant 0.2
embB 4247132 p.Asp207Asn missense_variant 0.12
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249560 p.Pro1016Gln missense_variant 0.13
aftB 4268005 c.832T>C synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0