TB-Profiler result

Run: SRR14782673
Summary

Run ID: SRR14782673

Sample name:

Date: 03-04-2023 11:34:42

Number of reads: 2950761

Percentage reads mapped: 99.7

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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.Ser450Cys missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.21
mshA 576113 p.Arg256Gly missense_variant 0.2
mshA 576450 p.Pro368Arg missense_variant 0.18
mshA 576456 p.Val370Gly missense_variant 0.35
mshA 576613 c.1266A>C synonymous_variant 0.25
mshA 576616 c.1269G>C synonymous_variant 0.28
rpoB 759862 p.Gln19Arg missense_variant 1.0
rpoB 762221 p.Glu805Asp missense_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.19
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.18
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.15
katG 2156196 c.-85C>T upstream_gene_variant 0.99
PPE35 2170065 p.Ala183Gly missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289040 c.187_201dupGACTATTCCTCGTCG conservative_inframe_insertion 0.95
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.18
folC 2746340 p.Ala420Val missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.18
Rv2752c 3066102 p.Asn30Lys missense_variant 0.98
thyA 3073868 p.Thr202Ala missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fbiD 3339734 p.Ala206Gly missense_variant 0.6
fbiD 3339751 p.Ala212Pro missense_variant 0.47
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.25
whiB7 3568428 c.252A>G synonymous_variant 0.42
whiB7 3568431 c.249C>G synonymous_variant 0.16
rpoA 3878641 c.-134C>G upstream_gene_variant 0.46
clpC1 4038287 c.2418C>T synonymous_variant 0.98
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.47
embB 4246529 p.Ser6Gly missense_variant 0.33
embB 4247016 p.Ser168Trp missense_variant 0.19
whiB6 4338594 c.-73T>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.98