TB-Profiler result

Run: SRR6046090
Summary

Run ID: SRR6046090

Sample name:

Date: 04-04-2023 12:11:10

Number of reads: 2017254

Percentage reads mapped: 97.39

Strain: lineage4.6

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
lineage4.6 Euro-American T;LAM None 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.11 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 8266 p.Ala322Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491349 c.567T>C synonymous_variant 1.0
rpoC 766586 p.Glu1073Lys missense_variant 1.0
mmpL5 775639 p.Ile948Val 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 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.12
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.12
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.13
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.13
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.14
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.14
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.13
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.12
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.11
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.11
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.98
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.11
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 0.98
katG 2154615 c.1497G>A synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4239706 c.-157A>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328245 c.-772C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407554 p.Arg217Trp missense_variant 1.0