TB-Profiler result

Run: ERR038755
Summary

Run ID: ERR038755

Sample name:

Date: 31-03-2023 08:42:49

Number of reads: 18083318

Percentage reads mapped: 99.46

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 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
rpoB 761155 p.Ser450Leu missense_variant 0.29 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.33 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 0.41 ethambutol
embA 4243222 c.-11C>A upstream_gene_variant 0.57 ethambutol
gid 4408087 c.115delC frameshift_variant 0.24 streptomycin
gid 4408100 c.102delG frameshift_variant 0.44 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
rpoC 762836 c.-534C>G upstream_gene_variant 0.26
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
atpE 1461019 c.-26C>A upstream_gene_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475615 n.1958C>T non_coding_transcript_exon_variant 0.98
rpsA 1833684 p.Arg48Pro missense_variant 1.0
rpsA 1834130 p.Glu197Lys missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.17
PPE35 2169866 c.747G>C synonymous_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.2
eis 2715586 c.-254G>C upstream_gene_variant 0.37
pepQ 2859381 c.1038C>G synonymous_variant 0.29
ribD 2987307 p.Ala157Pro missense_variant 0.16
Rv2752c 3064552 p.Arg547Pro missense_variant 0.25
thyX 3067901 c.45C>T synonymous_variant 0.99
thyA 3073806 c.666C>G synonymous_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642772 p.Asp413Ala missense_variant 0.16
rpoA 3877964 p.Arg182Trp missense_variant 0.18
clpC1 4038857 c.1848C>A synonymous_variant 0.28
clpC1 4039932 p.Gly258Val missense_variant 0.22
embC 4239842 c.-21C>A upstream_gene_variant 0.2
embC 4241292 p.Leu477Arg missense_variant 0.62
embC 4242425 p.Arg855Gly missense_variant 0.24
embC 4242476 p.Pro872Ala missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.99
embC 4242822 p.Val987Gly missense_variant 0.37
embA 4243622 c.390G>A synonymous_variant 1.0
embB 4247106 p.Pro198His missense_variant 0.6
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.23
ethA 4326279 p.Ser399Pro missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407862 p.Ile114Asn missense_variant 0.19