TB-Profiler result

Run: ERR2653070
Summary

Run ID: ERR2653070

Sample name:

Date: 31-03-2023 22:29:02

Number of reads: 1071145

Percentage reads mapped: 99.44

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 0.99
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 761155 p.Ser450Leu missense_variant 0.96 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289095 p.Asp49Glu missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326721 c.752dupG frameshift_variant 0.15 ethionamide, ethionamide
ethA 4326800 c.672_673dupGC frameshift_variant 0.33 ethionamide, ethionamide
ethA 4326885 c.587_588dupAC frameshift_variant 0.15 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
gyrB 5723 p.Ala162Ser missense_variant 1.0
gyrB 6009 p.Leu257Pro missense_variant 0.11
gyrB 6765 p.Leu509Pro missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7584 p.Ser95Ala missense_variant 0.88
gyrA 8040 p.Gly247Ser missense_variant 0.95
gyrA 8164 p.Ala288Asp missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575240 c.-108G>A upstream_gene_variant 1.0
mshA 575356 c.9T>C synonymous_variant 0.11
rpoB 761890 p.Val695Glu missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302822 c.-109T>C upstream_gene_variant 0.1
Rv1258c 1406404 p.Val313Ile missense_variant 0.33
atpE 1461156 p.Gly38Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474944 n.1287G>C non_coding_transcript_exon_variant 0.12
inhA 1674954 c.753G>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102885 p.Pro53Leu missense_variant 0.18
katG 2156244 c.-135_-134delCG upstream_gene_variant 0.14
PPE35 2170404 p.Ala70Gly missense_variant 0.11
PPE35 2170422 p.Ala64Gly missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2715168 c.165T>C synonymous_variant 0.17
folC 2746835 p.Ser255Leu missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087009 p.Val64Leu missense_variant 0.12
ald 3087619 c.801_802dupAG frameshift_variant 0.79
Rv3083 3449357 p.Asn285Ile missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640922 p.Gln127Arg missense_variant 0.17
rpoA 3878630 c.-123G>C upstream_gene_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040752 c.-48C>G upstream_gene_variant 0.11
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243159 c.-74C>T upstream_gene_variant 0.11
embA 4243814 c.585delT frameshift_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4246567 c.54G>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408313 c.-111A>G upstream_gene_variant 0.12