TB-Profiler result

Run: ERR11082301
Summary

Run ID: ERR11082301

Sample name:

Date: 10-04-2023 09:52:02

Number of reads: 508484

Percentage reads mapped: 99.46

Strain: lineage4.2.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.1 Euro-American LAM7-TUR None 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 761101 p.Gln432Pro missense_variant 1.0 rifampicin
katG 2154069 c.2042delA frameshift_variant 0.11 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
ethA 4327054 p.Tyr140* stop_gained 1.0 ethionamide
gid 4407851 c.351delG frameshift_variant 1.0 streptomycin
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 7505 c.204C>T synonymous_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8923 p.Gly541Asp missense_variant 0.12
gyrA 8934 p.Gln545* stop_gained 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575870 p.His175Tyr missense_variant 0.17
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576504 p.Thr386Ile missense_variant 1.0
ccsA 620346 c.456C>T synonymous_variant 0.11
rpoB 760676 p.Leu290Phe missense_variant 0.11
rpoC 764363 p.Gly332Cys missense_variant 1.0
rpoC 764904 p.Phe512Ser missense_variant 0.12
rpoC 765345 p.Gly659Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777744 p.Gly246Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304266 c.1339dupG frameshift_variant 0.11
fbiC 1305356 p.Gly809Asp missense_variant 0.17
Rv1258c 1407322 p.Gly7Ser missense_variant 0.12
atpE 1461034 c.-11A>G upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833526 c.-16G>A upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918563 c.624G>A synonymous_variant 0.11
ndh 2102343 p.Ala234Thr missense_variant 0.14
ndh 2102540 p.Ala168Val missense_variant 0.17
katG 2155528 p.Glu195Gly missense_variant 0.15
PPE35 2170054 p.Thr187Ser missense_variant 0.25
PPE35 2170234 c.378delT frameshift_variant 0.18
Rv1979c 2223152 p.Arg5Trp missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288942 c.300C>T synonymous_variant 0.11
pncA 2289000 p.Phe81Ser missense_variant 1.0
folC 2746465 c.1134G>A synonymous_variant 0.22
ribD 2987273 c.435C>A synonymous_variant 0.12
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087735 p.Pro306Ser missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474480 c.474C>T synonymous_variant 0.15
fbiB 3642556 p.Leu341Pro missense_variant 0.12
clpC1 4038936 p.Thr590Ile missense_variant 0.12
embC 4239672 c.-191G>A upstream_gene_variant 0.15
embC 4242107 p.Cys749Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267709 c.1128C>T synonymous_variant 0.25
aftB 4267811 c.1026G>A synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0