TB-Profiler result

Run: ERR046977
Summary

Run ID: ERR046977

Sample name:

Date: 31-03-2023 08:59:41

Number of reads: 6940596

Percentage reads mapped: 99.73

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761161 p.Leu452Pro missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289164 c.77delC frameshift_variant 0.49 pyrazinamide
pncA 2289248 c.-7T>C upstream_gene_variant 0.17 pyrazinamide
embB 4247729 p.Gly406Ser 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 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.39
rpoC 762836 c.-534C>G upstream_gene_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.24
inhA 1674892 p.Asn231Asp missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.23
ndh 2102891 p.Phe51Ser missense_variant 0.3
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169379 p.Phe412Val missense_variant 0.25
PPE35 2169866 c.747G>C synonymous_variant 0.55
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.29
ahpC 2726151 c.-42T>C upstream_gene_variant 1.0
folC 2747263 c.336C>A synonymous_variant 0.16
folC 2747478 p.Thr41Pro missense_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.21
ribD 2987307 p.Ala157Pro missense_variant 0.14
Rv2752c 3064741 p.Gly484Ala missense_variant 0.25
thyX 3067995 c.-50A>C upstream_gene_variant 0.21
thyA 3073806 c.666C>G synonymous_variant 0.26
fbiD 3339273 c.156T>G synonymous_variant 0.32
fbiD 3339550 p.Gly145Trp missense_variant 0.2
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.2
fbiB 3642734 c.1200G>C synonymous_variant 0.19
fbiB 3642772 p.Asp413Ala missense_variant 0.25
ddn 3987013 p.Gly57Ala missense_variant 0.24
clpC1 4038857 c.1848C>A synonymous_variant 0.17
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039932 p.Gly258Val missense_variant 0.35
panD 4043905 p.Glu126Val missense_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.38
embC 4242827 p.Leu989Val missense_variant 0.19
ubiA 4269529 p.Ala102Gly missense_variant 0.18
ethA 4327672 c.-199G>A upstream_gene_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408061 p.His48Asn missense_variant 1.0
Rv3083 3448497 c.-6_*1430del transcript_ablation 1.0