TB-Profiler result

Run: SRR8651581
Summary

Run ID: SRR8651581

Sample name:

Date: 04-04-2023 21:46:23

Number of reads: 6022216

Percentage reads mapped: 85.15

Strain: lineage4.5

Drug-resistance: Pre-XDR-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
lineage4.5 Euro-American H;T RD122 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
gyrA 7564 p.Gly88Ala missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155289 p.Thr275Pro missense_variant 1.0 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
ethA 4326665 c.808dupC frameshift_variant 0.68 ethionamide
ethA 4326852 c.620_621dupGC frameshift_variant 0.34 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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576386 c.1040dupC frameshift_variant 0.99
ccsA 620029 c.139C>T synonymous_variant 0.99
rpoB 761496 p.Tyr564His missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778990 p.Val1Leu missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
Rv1258c 1407363 c.-23C>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.1
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.11
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.11
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.11
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.14
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
rpsA 1834165 c.624A>G synonymous_variant 1.0
rpsA 1834338 p.Asp266Ala missense_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289081 p.Pro54Arg missense_variant 1.0
eis 2715076 p.Ala86Val missense_variant 0.98
Rv2752c 3066155 c.36dupC frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 0.86
rpoA 3878626 c.-119A>G upstream_gene_variant 0.14
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269299 p.Ile179Leu missense_variant 0.99
ethA 4326066 p.Arg470Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0