TB-Profiler result

Run: SRR6797613
Summary

Run ID: SRR6797613

Sample name:

Date: 04-04-2023 16:13:56

Number of reads: 1115046

Percentage reads mapped: 95.68

Strain: lineage4.3.4.2

Drug-resistance: Other

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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
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.97
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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.17 kanamycin, capreomycin, aminoglycosides, amikacin
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 8839 p.Arg513Leu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
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
rplC 801207 c.399C>A synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.14
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.19
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.1
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.1
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.1
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.1
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.1
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.1
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.12
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.14
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.1
rrs 1473179 n.1334C>A non_coding_transcript_exon_variant 0.11
rrs 1473189 n.1344C>A non_coding_transcript_exon_variant 0.12
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.18
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167791 p.Ser941Tyr missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2222065 p.Leu367Pro missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.25
Rv2752c 3065293 p.Val300Ala missense_variant 0.94
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087852 p.Thr345Ser missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3878702 c.-195T>C upstream_gene_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_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 1.0