TB-Profiler result

Run: ERR4799300
Summary

Run ID: ERR4799300

Sample name:

Date: 01-04-2023 09:01:12

Number of reads: 2910789

Percentage reads mapped: 99.66

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.98
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 7582 p.Asp94Ala missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2288779 p.Val155Met missense_variant 0.99 pyrazinamide
embB 4248002 p.Gln497Lys missense_variant 0.98 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 5332 c.93C>T synonymous_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8168 p.Glu289Asp missense_variant 1.0
rpoC 765612 p.His748Pro missense_variant 0.99
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747470 p.Ile43Ala missense_variant 0.98
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.71
Rv3083 3448500 c.-4A>G upstream_gene_variant 0.6
Rv3083 3448501 c.-3G>T upstream_gene_variant 0.6
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245417 p.Gly729Arg missense_variant 0.99
ubiA 4269298 p.Ile179Thr missense_variant 0.98
ethA 4327301 p.Asp58Gly missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0