TB-Profiler result

Run: SRR6832303

Summary

Run ID: SRR6832303

Sample name:

Date: 04-04-2023 17:21:03

Number of reads: 649090

Percentage reads mapped: 99.67

Strain: 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 1.0
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 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
gyrB 5258 p.Lys7* stop_gained 0.18
gyrB 5275 c.36C>T synonymous_variant 0.17
gyrB 6152 p.Ala305Thr missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7565 c.264C>A synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7787 p.Glu162Asp missense_variant 0.25
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 763788 p.Asp140Val missense_variant 0.22
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
rpsL 781644 p.Gln29* stop_gained 0.2
fbiC 1303968 c.1038G>T synonymous_variant 0.13
fbiC 1304131 p.Ala401Thr missense_variant 0.5
Rv1258c 1407155 c.186C>T synonymous_variant 0.25
embR 1416589 c.759G>T synonymous_variant 0.15
atpE 1461276 p.Thr78Ala missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472765 n.920G>T non_coding_transcript_exon_variant 0.13
rrs 1472796 n.951A>T non_coding_transcript_exon_variant 0.12
rrl 1475678 n.2021A>G non_coding_transcript_exon_variant 0.17
rpsA 1833512 c.-30A>C upstream_gene_variant 0.29
rpsA 1834224 p.Leu228His missense_variant 0.17
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2170626 c.-14G>A upstream_gene_variant 0.17
Rv1979c 2223110 p.Val19Ile missense_variant 0.4
Rv1979c 2223275 c.-111C>T upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289129 p.Ala38Gly missense_variant 0.4
kasA 2518911 p.Leu266Pro missense_variant 0.17
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726194 c.2T>C start_lost 0.15
folC 2746340 p.Ala420Val missense_variant 1.0
folC 2747065 c.533delG frameshift_variant 0.14
Rv2752c 3066007 p.Pro62Leu missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074509 c.-38G>T upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449902 p.Glu467Lys missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877738 p.Thr257Met missense_variant 0.29
clpC1 4038234 p.Arg824Leu missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4040537 c.168G>A synonymous_variant 0.2
embC 4239780 c.-83G>A upstream_gene_variant 0.2
embC 4242116 p.Ala752Thr missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243410 p.Ala60Thr missense_variant 0.18
embB 4248729 p.Asn739Thr missense_variant 0.4
aftB 4267053 p.Tyr595Cys missense_variant 0.11
ethA 4326242 p.Asp411Gly missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0