TB-Profiler result

Run: ERR040134
Summary

Run ID: ERR040134

Sample name:

Date: 31-03-2023 08:47:51

Number of reads: 20179096

Percentage reads mapped: 99.53

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289030 p.His71Arg missense_variant 0.33 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 0.97 ethambutol
ethA 4327033 p.Tyr147* stop_gained 1.0 ethionamide
ethA 4327054 p.Tyr140* stop_gained 0.22 ethionamide
ethA 4326694 c.440_779del frameshift_variant 1.0 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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.22
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.29
rpoC 764725 p.Phe452Leu missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765627 p.Ala753Glu missense_variant 1.0
rpoC 767083 c.3714C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303174 p.Leu82Val missense_variant 0.29
atpE 1461019 c.-26C>A upstream_gene_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.99
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.2
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.26
inhA 1674892 p.Asn231Asp missense_variant 0.17
inhA 1674952 p.Pro251Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.19
PPE35 2169866 c.747G>C synonymous_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.22
folC 2746186 c.1413G>C synonymous_variant 0.3
pepQ 2859381 c.1038C>G synonymous_variant 0.22
ribD 2987307 p.Ala157Pro missense_variant 0.17
Rv2752c 3064552 p.Arg547Pro missense_variant 0.25
thyA 3073806 c.666C>G synonymous_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.99
fbiB 3642734 c.1200G>C synonymous_variant 0.19
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840869 c.552C>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.31
embC 4242425 p.Arg855Gly missense_variant 0.49
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.39
embC 4242827 p.Leu989Val missense_variant 0.17
embA 4244375 c.1143C>G synonymous_variant 0.26
ubiA 4269529 p.Ala102Gly missense_variant 0.22
ethA 4326695 p.Met260Lys missense_variant 0.86
ethA 4327672 c.-199G>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408057 p.Leu49Pro missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0