TB-Profiler result

Run: ERR5865968
Summary

Run ID: ERR5865968

Sample name:

Date: 02-04-2023 00:25:07

Number of reads: 4650315

Percentage reads mapped: 89.77

Strain: lineage4.8

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Gly missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol
gid 4408087 c.115delC frameshift_variant 0.99 streptomycin
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 5499 p.Ala87Asp missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7724 p.Met141Ile missense_variant 0.97
fgd1 490829 p.Ala16Val missense_variant 0.99
rpoC 767123 p.Val1252Met missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775677 p.Lys935Thr missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.28
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 0.99
ndh 2103202 c.-160C>T upstream_gene_variant 0.15
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.75
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4269546 c.-710G>C upstream_gene_variant 0.96
ubiA 4269864 c.-31C>T upstream_gene_variant 0.95
ethA 4327006 p.Asp156Glu missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448444 c.-59_*1408del transcript_ablation 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0