TB-Profiler result

Run: SRR4034160
Summary

Run ID: SRR4034160

Sample name:

Date: 04-04-2023 06:36:18

Number of reads: 1210915

Percentage reads mapped: 99.79

Strain: lineage4.3.3

Drug-resistance: HR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
katG 2153990 c.2121delT frameshift_variant 0.14 isoniazid
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 5256 p.Lys6Arg missense_variant 0.1
gyrB 5477 p.Asp80Asn missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.93
gyrA 9077 c.1776C>T synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761564 c.1758G>T synonymous_variant 0.11
rpoC 762473 c.-897C>A upstream_gene_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775926 c.2554delC frameshift_variant 0.25
mmpL5 777218 c.1263G>A synonymous_variant 0.12
mmpR5 778313 c.-677G>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302869 c.-62G>A upstream_gene_variant 0.11
fbiC 1304037 c.1107G>A synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rpsA 1833783 p.Ser81Phe missense_variant 0.13
tlyA 1917917 c.-23G>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102412 p.Val211Met missense_variant 0.1
PPE35 2170400 c.212delC frameshift_variant 0.17
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223096 c.69G>A synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2715416 c.-84C>A upstream_gene_variant 0.11
eis 2715506 c.-175delG upstream_gene_variant 0.17
ahpC 2726313 p.Asp41Tyr missense_variant 0.1
folC 2747532 p.Glu23Lys missense_variant 0.12
ribD 2987107 p.Ile90Thr missense_variant 0.15
ribD 2987580 p.Ser248Thr missense_variant 0.33
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449062 p.Ala187Ser missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641508 c.969delG frameshift_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039575 p.Ala377Val missense_variant 0.12
clpC1 4039683 p.Arg341His missense_variant 0.11
clpC1 4040257 p.Ala150Thr missense_variant 0.22
embC 4239850 c.-13A>G upstream_gene_variant 0.15
embC 4240067 c.208_209delGT frameshift_variant 0.12
embC 4241712 p.Arg617Gln missense_variant 0.12
embC 4242425 p.Arg855Gly missense_variant 0.33
embC 4242579 p.Ala906Val missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245475 p.Gly748Asp missense_variant 0.13
embB 4249661 p.Ala1050Thr missense_variant 0.13
embB 4249787 p.Gly1092Ser missense_variant 0.11
aftB 4268775 p.Ser21Asn missense_variant 0.11
aftB 4268913 c.-77A>T upstream_gene_variant 0.12
ethR 4326787 c.-762C>A upstream_gene_variant 0.12
ethA 4328291 c.-818C>A upstream_gene_variant 0.11
ethA 4328318 c.-845G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0