TB-Profiler result

Run: SRR12830378
Summary

Run ID: SRR12830378

Sample name:

Date: 03-04-2023 06:58:42

Number of reads: 446086

Percentage reads mapped: 99.77

Strain: lineage4.3.3

Drug-resistance: Sensitive

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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
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 8194 p.Gly298Asp missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9382 p.Gly694Val missense_variant 0.12
rpoB 762006 p.Arg734Gly missense_variant 0.12
rpoC 763247 c.-123G>A upstream_gene_variant 0.13
rpoC 763824 p.Glu152Gly missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779298 c.-818G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303350 p.Cys140* stop_gained 0.15
embR 1417524 c.-177G>T upstream_gene_variant 0.22
atpE 1460944 c.-101T>A upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472180 n.335A>G non_coding_transcript_exon_variant 0.22
rrl 1473514 n.-144C>T upstream_gene_variant 0.29
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 1.0
rrl 1475239 n.1582A>C non_coding_transcript_exon_variant 0.29
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.12
inhA 1673408 c.-794G>T upstream_gene_variant 0.11
inhA 1673832 c.-370A>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102308 c.735G>A synonymous_variant 1.0
ndh 2103197 c.-155T>C upstream_gene_variant 0.15
katG 2154008 p.Ser702Thr missense_variant 0.12
katG 2154233 p.Leu627Met missense_variant 0.12
katG 2155578 p.Phe178Leu missense_variant 0.13
PPE35 2169497 c.1116C>T synonymous_variant 0.18
PPE35 2169608 c.1005C>T synonymous_variant 0.25
Rv1979c 2221884 c.1281G>T synonymous_variant 0.14
Rv1979c 2222960 p.Ala69Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
pepQ 2859671 p.Tyr250His missense_variant 0.11
Rv2752c 3066064 p.Ile43Asn missense_variant 0.13
thyX 3067717 p.Ser77Gly missense_variant 0.1
thyX 3067887 p.Pro20Gln missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449854 p.Met451Val missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641930 p.Leu132Phe missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249606 c.3093C>T synonymous_variant 0.15
ethA 4326569 p.Phe302Ser missense_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 1.0