TB-Profiler result

Run: ERR2516485
Summary

Run ID: ERR2516485

Sample name:

Date: 31-03-2023 21:33:57

Number of reads: 3946586

Percentage reads mapped: 99.67

Strain: lineage4.3.4.2;lineage4.1.2.1

Drug-resistance: Pre-XDR-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 0.45
lineage4.1 Euro-American T;X;H None 0.55
lineage4.1.2 Euro-American T;H None 0.57
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.55
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.43
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
gyrB 6735 p.Asn499Thr missense_variant 0.59 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.32 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.62 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Pro missense_variant 0.68 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.5 rifampicin
rpoC 764948 p.Leu527Val missense_variant 0.47 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288697 p.Leu182Ser missense_variant 0.56 pyrazinamide
pncA 2288973 p.Ile90Thr missense_variant 0.36 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.58 isoniazid
embB 4247431 p.Met306Ile 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 6140 p.Val301Leu missense_variant 0.44
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.57
mshA 575679 p.Asn111Ser missense_variant 0.59
rpoB 760115 c.309C>T synonymous_variant 0.68
rpoC 764817 p.Val483Gly missense_variant 0.63
rpoC 764995 c.1626C>G synonymous_variant 0.45
rpoC 765150 p.Gly594Glu missense_variant 0.61
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833469 c.-73G>T upstream_gene_variant 0.52
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.59
ahpC 2726388 p.Ala66Thr missense_variant 0.11
ribD 2987307 p.Ala157Pro missense_variant 0.16
thyA 3073806 c.666C>G synonymous_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.49
Rv3236c 3612846 p.Pro91Ser missense_variant 0.48
alr 3840719 c.702A>G synonymous_variant 0.43
clpC1 4038287 c.2418C>T synonymous_variant 0.5
panD 4044181 p.Asp34Gly missense_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.44
embB 4248004 p.Gln497His missense_variant 0.47
ubiA 4269671 p.Val55Leu missense_variant 0.47
ethA 4326182 p.Phe431Ser missense_variant 0.58
ethA 4326705 p.Pro257Ala missense_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 0.55
gid 4407691 p.Val171Gly missense_variant 0.54
gid 4407970 p.Pro78Leu missense_variant 0.42
gid 4408156 p.Leu16Arg missense_variant 0.45