TB-Profiler result

Run: ERR4132450
Summary

Run ID: ERR4132450

Sample name:

Date: 01-04-2023 04:30:31

Number of reads: 366672

Percentage reads mapped: 99.48

Strain: lineage4.3.3

Drug-resistance: MDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 1.0
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 761139 p.His445Asp missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289126 c.115dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 1.0 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 6570 p.Asp444Gly missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490715 c.-68A>G upstream_gene_variant 0.15
rpoC 763615 c.246G>A synonymous_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766958 p.Gly1197Cys missense_variant 0.4
rpoC 767282 p.Val1305Ile missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776003 c.2478C>T synonymous_variant 0.17
mmpL5 776008 p.His825Asp missense_variant 0.15
mmpL5 776009 c.2472A>G synonymous_variant 0.17
mmpL5 777286 p.Ala399Thr missense_variant 0.2
mmpL5 778753 c.-273C>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302987 c.57C>G synonymous_variant 0.18
fbiC 1303016 p.Val29Gly missense_variant 0.33
fbiC 1303095 c.165G>A synonymous_variant 1.0
fbiC 1304247 c.1317C>T synonymous_variant 0.33
fbiC 1304525 p.Ala532Asp missense_variant 0.67
fbiC 1304962 p.Trp678Gly missense_variant 1.0
embR 1416344 p.Thr335Met missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.46
fabG1 1673942 p.Ala168Val missense_variant 0.17
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155693 p.Ser140Ile missense_variant 0.17
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289302 c.-62delT upstream_gene_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.18
kasA 2518882 c.768C>A synonymous_variant 0.18
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714508 c.825A>G synonymous_variant 0.25
eis 2714887 p.Phe149Ser missense_variant 0.33
eis 2715432 c.-100C>T upstream_gene_variant 0.22
eis 2715436 c.-104G>A upstream_gene_variant 0.2
eis 2715440 c.-108A>C upstream_gene_variant 0.22
eis 2715445 c.-113C>T upstream_gene_variant 0.22
eis 2715447 c.-115T>A upstream_gene_variant 0.22
eis 2715450 c.-118T>C upstream_gene_variant 0.22
eis 2715451 c.-119C>A upstream_gene_variant 0.22
eis 2715454 c.-122T>G upstream_gene_variant 0.22
eis 2715455 c.-123G>A upstream_gene_variant 0.22
eis 2715458 c.-126T>A upstream_gene_variant 0.22
eis 2715460 c.-128A>G upstream_gene_variant 0.22
eis 2715465 c.-133G>T upstream_gene_variant 0.22
eis 2715469 c.-137T>C upstream_gene_variant 0.18
eis 2715473 c.-141A>G upstream_gene_variant 0.2
ahpC 2726341 p.Val50Gly missense_variant 0.36
folC 2746340 p.Ala420Val missense_variant 1.0
folC 2747535 p.Asp22Asn missense_variant 0.18
pepQ 2859533 p.His296Tyr missense_variant 0.18
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3066290 c.-99G>T upstream_gene_variant 0.13
Rv2752c 3066336 c.-145C>A upstream_gene_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086799 c.-21A>G upstream_gene_variant 0.12
Rv3083 3448673 p.Ser57Tyr missense_variant 0.5
Rv3083 3449702 p.Asp400Val missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612322 c.794delC frameshift_variant 0.18
fbiB 3642130 p.Ala199Asp missense_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embC 4240121 p.Pro87Ser missense_variant 0.2
embC 4240698 p.Ala279Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Gln missense_variant 0.2
embB 4247937 p.Thr475Lys missense_variant 0.29
aftB 4267737 p.Thr367Ile missense_variant 0.14
ubiA 4269775 p.Ala20Glu missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338665 c.-144C>A upstream_gene_variant 0.13
gid 4407776 p.Asp143Tyr missense_variant 0.14
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408381 c.-179A>C upstream_gene_variant 0.2