TB-Profiler result

Run: ERR2516132
Summary

Run ID: ERR2516132

Sample name:

Date: 31-03-2023 21:19:48

Number of reads: 748368

Percentage reads mapped: 99.23

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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
gyrA 7585 p.Ser95Thr missense_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575857 c.510G>A synonymous_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779185 p.Gly66Trp missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407489 c.-149G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
rpsA 1834438 c.897C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918106 p.Thr56Ile missense_variant 0.13
katG 2154900 c.1212G>A synonymous_variant 0.12
katG 2155552 p.Arg187Leu missense_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
Rv2752c 3066299 c.-108C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449396 p.Cys298Phe missense_variant 0.12
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
fprA 3474594 c.588C>T synonymous_variant 0.12
fprA 3474856 p.Val284Leu missense_variant 0.13
fprA 3475205 p.Glu400Val missense_variant 0.25
fbiA 3641309 p.Ala256Gly missense_variant 0.12
fbiB 3642148 p.Val205Ala missense_variant 0.15
fbiB 3642692 c.1158C>A synonymous_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.92
embA 4244930 c.1698G>A synonymous_variant 0.22
embA 4245305 c.2075_2076dupTG frameshift_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.36
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.13
embB 4246556 p.Ala15Pro missense_variant 0.13
embB 4246563 p.Leu17Trp missense_variant 0.13
embB 4246567 c.54G>T synonymous_variant 0.13
ubiA 4268929 p.Gly302Val missense_variant 0.12
whiB6 4338189 c.333G>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0