TB-Profiler result

Run: ERR9993029
Summary

Run ID: ERR9993029

Sample name:

Date: 02-04-2023 14:00:31

Number of reads: 2542950

Percentage reads mapped: 75.24

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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761161 p.Leu452Pro missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 0.99 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.34
rpoB 762889 p.His1028Arg missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778994 p.Ser2Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.23
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.23
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.22
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.24
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.26
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.23
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.22
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.21
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.21
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.2
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.19
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.19
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.16
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.12
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.12
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.13
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.12
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.13
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.1
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.1
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.11
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.1
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.12
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.11
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
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
rpoA 3878583 c.-76C>A upstream_gene_variant 0.25
rpoA 3878609 c.-102T>A upstream_gene_variant 0.27
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.98
gid 4407912 c.160_290del frameshift_variant 1.0