TB-Profiler result

Run: SRR6485055
Summary

Run ID: SRR6485055

Sample name:

Date: 04-04-2023 15:04:21

Number of reads: 1795144

Percentage reads mapped: 99.5

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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
gyrB 6579 p.Ser447Phe missense_variant 0.69 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576482 p.Val379Leu missense_variant 0.18
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 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673357 c.-83G>A upstream_gene_variant 0.1
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746136 c.1463G>A splice_region_variant&stop_retained_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.11
clpC1 4039729 p.Asp326Asn missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.38
ethA 4326078 p.Arg466Trp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408070 p.Trp45Arg missense_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0