TB-Profiler result

Run: SRR18715352
Summary

Run ID: SRR18715352

Sample name:

Date: 03-04-2023 20:30:07

Number of reads: 3168707

Percentage reads mapped: 99.74

Strain: lineage4.8;lineage4.3.3

Drug-resistance: HR-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 0.24
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.74
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.26
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
rpsL 781687 p.Lys43Arg missense_variant 0.54 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.74 isoniazid, ethionamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.56 isoniazid
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 0.29
gyrA 8040 p.Gly247Ser missense_variant 0.26
gyrA 9304 p.Gly668Asp missense_variant 0.24
mshA 576108 p.Ala254Gly missense_variant 0.16
mshA 576453 p.Val369Gly missense_variant 0.21
mshA 576616 c.1269G>C synonymous_variant 0.25
rpoC 764367 p.Gly333Ala missense_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 0.2
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
rpsL 781676 c.117C>T synonymous_variant 0.54
fbiC 1305105 c.2175G>A synonymous_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.19
fabG1 1673553 p.Asp38Glu missense_variant 0.28
rpsA 1834836 p.Met432Thr missense_variant 0.25
tlyA 1917811 c.-129T>C upstream_gene_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155751 p.Gly121Ser missense_variant 0.64
katG 2156196 c.-85C>T upstream_gene_variant 0.17
PPE35 2168149 p.Pro822Ser missense_variant 0.24
PPE35 2170065 p.Ala183Gly missense_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.31
folC 2746340 p.Ala420Val missense_variant 0.16
pepQ 2860159 p.Ala87Gly missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 0.21
ald 3087816 p.Cys333Gly missense_variant 0.18
fbiD 3339734 p.Ala206Gly missense_variant 0.4
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.21
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.12
Rv3083 3448631 p.Gly43Asp missense_variant 0.11
Rv3083 3449845 p.Gln448Glu missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.16
whiB7 3568428 c.252A>G synonymous_variant 0.5
whiB7 3568431 c.249C>G synonymous_variant 0.21
rpoA 3878597 c.-90G>C upstream_gene_variant 0.4
rpoA 3878641 c.-134C>G upstream_gene_variant 0.77
clpC1 4038287 c.2418C>T synonymous_variant 0.25
clpC1 4038968 c.1737G>A synonymous_variant 0.22
embC 4240409 p.Pro183Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.23
embB 4248328 c.1815G>C synonymous_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407992 p.Gly71Arg missense_variant 0.2
gid 4408061 p.His48Tyr missense_variant 0.2
gid 4408156 p.Leu16Arg missense_variant 0.32