TB-Profiler result

Run: ERR4972584
Summary

Run ID: ERR4972584

Sample name:

Date: 01-04-2023 21:47:47

Number of reads: 646773

Percentage reads mapped: 99.44

Strain: lineage4.3.2

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
lineage4.3.2 Euro-American (LAM) LAM3 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288930 p.Ser104Arg missense_variant 1.0 pyrazinamide
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490757 c.-26T>A upstream_gene_variant 1.0
mshA 575672 p.Val109Met missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.2
ccsA 620461 p.Val191Ile missense_variant 0.14
rpoB 761607 p.Met601Val missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766337 p.Asp990Asn missense_variant 0.13
rpoC 766933 c.3564A>C synonymous_variant 0.13
rpoC 767041 c.3672G>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801440 c.633dupG frameshift_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472881 n.1036C>T non_coding_transcript_exon_variant 0.25
rpsA 1834551 p.Val337Glu missense_variant 0.11
tlyA 1917926 c.-14G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170157 p.Ala152Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715473 c.-141A>G upstream_gene_variant 0.12
Rv2752c 3065453 p.Gln247* stop_gained 1.0
Rv2752c 3066212 c.-22delT upstream_gene_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087830 c.1011G>A synonymous_variant 0.15
Rv3083 3449376 c.873G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841072 p.Gly117Ser missense_variant 0.15
clpC1 4038245 p.Phe820Leu missense_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039306 c.1398dupG frameshift_variant 0.12
clpC1 4039968 p.Gln246Leu missense_variant 0.11
clpC1 4040057 c.648C>T synonymous_variant 0.17
embC 4242252 p.Asp797Gly missense_variant 0.14
embC 4242402 p.Arg847His missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243651 p.His140Leu missense_variant 0.11
embB 4245803 c.-711C>T upstream_gene_variant 0.14
embB 4248324 p.Ala604Gly missense_variant 0.2
ubiA 4269734 p.Ala34Thr missense_variant 0.12
ethR 4327441 c.-108G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407980 p.Pro75Ser missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0