TB-Profiler result

Run: ERR10877882
Summary

Run ID: ERR10877882

Sample name:

Date: 31-03-2023 11:21:55

Number of reads: 3346755

Percentage reads mapped: 99.64

Strain: lineage4.3.3;lineage4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.76
lineage4.2 Euro-American H;T;LAM None 0.21
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.2
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.78
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 0.73 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.83 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.82 isoniazid, ethionamide
tlyA 1918160 p.Leu74Pro missense_variant 0.73 capreomycin
katG 2155168 p.Ser315Thr missense_variant 0.86 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 0.78 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.72 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.78
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.12
mshA 576488 p.Val381His missense_variant 0.17
rpoC 764931 p.Ala521Asp missense_variant 0.75
rpoC 764995 c.1626C>G synonymous_variant 0.76
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.8
fbiC 1304962 p.Trp678Gly missense_variant 0.81
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.21
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.21
rpsA 1834836 p.Met432Thr missense_variant 0.73
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.85
PPE35 2169879 p.Phe245Cys missense_variant 0.25
PPE35 2170035 p.Val193Ala missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.32
PPE35 2170053 p.Thr187Ser missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.68
folC 2746340 p.Ala420Val missense_variant 0.73
ribD 2986827 c.-12G>A upstream_gene_variant 0.84
thyA 3073868 p.Thr202Ala missense_variant 0.72
thyA 3073914 p.His186Gln missense_variant 0.21
ald 3086742 c.-78A>C upstream_gene_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>T synonymous_variant 0.2
fbiD 3339744 c.627A>C synonymous_variant 0.21
fbiD 3339753 c.636A>G synonymous_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.47
rpoA 3878578 c.-71C>A upstream_gene_variant 0.18
rpoA 3878599 c.-92C>G upstream_gene_variant 0.27
rpoA 3878639 c.-132C>G upstream_gene_variant 0.13
ddn 3987233 c.390C>T synonymous_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 0.79
clpC1 4038968 c.1737G>A synonymous_variant 0.72
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.35
embB 4246548 p.Pro12Gln missense_variant 0.49
embB 4246555 c.42G>C synonymous_variant 0.48
embB 4246556 p.Ala15Pro missense_variant 0.49
embB 4246563 p.Leu17Trp missense_variant 0.47
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4249594 c.3081G>A synonymous_variant 0.31
ethA 4328376 c.-903G>C upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.84