TB-Profiler result

Run: ERR4020182
Summary

Run ID: ERR4020182

Sample name:

Date: 01-04-2023 03:59:32

Number of reads: 3610510

Percentage reads mapped: 99.73

Strain: lineage4.4.1.1;lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.2
lineage4.4 Euro-American S;T None 0.78
lineage4.4.1 Euro-American (S-type) S;T None 0.79
lineage4.3.4 Euro-American (LAM) LAM RD174 0.2
lineage4.4.1.1 Euro-American S;Orphans None 0.77
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.21
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.19
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 761108 p.Met434Ile missense_variant 0.78 rifampicin
rpoB 761155 p.Ser450Trp missense_variant 0.24 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 0.72 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.16 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Asp missense_variant 0.84 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.21 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 0.26
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 0.83
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.23
mshA 576482 p.Val379Leu missense_variant 0.17
rpoB 761406 p.Val534Met missense_variant 0.88
rpoB 761558 c.1752C>G synonymous_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 0.79
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406353 p.Pro330Thr missense_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.81
PPE35 2168479 p.Thr712Pro missense_variant 0.75
PPE35 2169840 p.Gly258Asp missense_variant 0.76
PPE35 2170065 p.Ala183Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518496 c.382C>T synonymous_variant 0.8
Rv2752c 3065023 p.Pro390Leu missense_variant 0.84
thyA 3073868 p.Thr202Ala missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.33
Rv3083 3448522 p.Val7Phe missense_variant 0.78
Rv3083 3448608 c.105G>A synonymous_variant 0.81
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.8
Rv3236c 3612009 p.Ala370Thr missense_variant 0.2
Rv3236c 3612665 p.Val151Ala missense_variant 0.73
alr 3840719 c.702A>G synonymous_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.39
embB 4248324 p.Ala604Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.27