TB-Profiler result

Run: SRR6824541
Summary

Run ID: SRR6824541

Sample name:

Date: 04-04-2023 16:45:17

Number of reads: 10304340

Percentage reads mapped: 99.17

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 0.13 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.51 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.67 rifampicin
katG 2156089 c.22dupA frameshift_variant 0.69 isoniazid, isoniazid
pncA 2288934 p.Tyr103Ser missense_variant 0.67 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.65 ethambutol
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
gyrB 5103 c.-137C>T upstream_gene_variant 0.11
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
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 761518 p.Asp571Ala missense_variant 0.51
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
rrl 1473635 n.-23A>G upstream_gene_variant 0.74
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
folC 2747323 c.276C>T synonymous_variant 0.15
Rv2752c 3065488 p.Val235Gly missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841329 p.Thr31Ile missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.16
alr 3841612 c.-193_-192insC upstream_gene_variant 0.16
rpoA 3878575 c.-68C>T upstream_gene_variant 0.98
clpC1 4038318 p.Pro796Leu missense_variant 1.0
clpC1 4040498 c.207G>A synonymous_variant 0.91
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243760 p.Asp176Glu missense_variant 0.94
embB 4248757 c.2244A>C synonymous_variant 0.18
aftB 4267964 c.873T>G synonymous_variant 0.65
whiB6 4338595 c.-75delG upstream_gene_variant 1.0