TB-Profiler result

Run: ERR4972574
Summary

Run ID: ERR4972574

Sample name:

Date: 01-04-2023 21:47:31

Number of reads: 359038

Percentage reads mapped: 19.98

Strain: lineage4.1.2.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9783 p.Val828Met missense_variant 0.15
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 763504 c.135C>G synonymous_variant 0.18
rpoC 763507 c.138G>C synonymous_variant 0.2
rpoC 763528 c.159G>T synonymous_variant 0.22
rpoC 763534 c.165T>C synonymous_variant 0.2
rpoC 763537 c.168C>G synonymous_variant 0.2
rpoC 763546 c.177A>G synonymous_variant 0.13
rpoC 763570 c.201G>C synonymous_variant 0.13
rpoC 763573 c.204G>C synonymous_variant 0.13
rpoC 763576 c.207C>G synonymous_variant 0.13
rpoC 763603 c.234C>T synonymous_variant 0.13
rpoC 763609 c.240C>G synonymous_variant 0.13
rpoC 763615 c.246G>C synonymous_variant 0.13
rpoC 763633 c.264T>C synonymous_variant 0.13
rpoC 764862 p.Leu498Pro missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777793 p.Ala230Thr missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303105 p.Cys59Ser missense_variant 0.18
embR 1417124 p.Tyr75Phe missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472771 n.926G>A non_coding_transcript_exon_variant 0.14
rrl 1475240 n.1583C>A non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102067 p.Val326Leu missense_variant 0.25
ndh 2102204 c.838delG frameshift_variant 0.15
PPE35 2169751 p.Gly288* stop_gained 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518116 p.Val1Ala missense_variant 0.11
Rv2752c 3065853 c.339A>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087792 p.Ala325Thr missense_variant 0.17
Rv3083 3449906 p.Lys468Arg missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.5
embB 4247028 p.Leu172Arg missense_variant 0.33
embB 4248319 c.1806A>T synonymous_variant 0.2
embB 4249353 p.Arg947Gln missense_variant 0.12
ubiA 4269122 p.Phe238Val missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408424 c.-222C>G upstream_gene_variant 0.22