TB-Profiler result

Run: ERR2864249
Summary

Run ID: ERR2864249

Sample name:

Date: 31-03-2023 23:54:35

Number of reads: 554691

Percentage reads mapped: 99.82

Strain: lineage4.3.4.2

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
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, 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 6817 c.-485G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759744 c.-62delC upstream_gene_variant 0.1
rpoB 762517 p.Gly904Val missense_variant 0.11
rpoB 763188 p.Asn1128Asp missense_variant 0.12
rpoC 764706 p.Leu446Pro missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471862 n.17T>C non_coding_transcript_exon_variant 0.11
rrl 1475120 n.1463G>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918184 p.Ala82Val missense_variant 0.11
tlyA 1918187 p.Gly83Asp missense_variant 0.11
tlyA 1918210 p.Ala91Thr missense_variant 0.12
PPE35 2169945 p.Gly223Glu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3067118 c.-927A>G upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 0.94
thyA 3074538 c.-67T>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086971 p.Lys51Met missense_variant 0.1
fbiD 3339546 c.429G>A synonymous_variant 0.14
Rv3083 3448345 c.-159G>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474914 p.Ala303Val missense_variant 0.12
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3877952 p.Arg186Ser missense_variant 0.38
rpoA 3877971 p.Asp179Glu missense_variant 0.18
rpoA 3878173 p.Pro112Gln missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4043925 c.357C>T synonymous_variant 0.12
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244822 c.1590G>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0