TB-Profiler result

Run: ERR4972533
Summary

Run ID: ERR4972533

Sample name:

Date: 01-04-2023 21:45:51

Number of reads: 603717

Percentage reads mapped: 99.11

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 Euro-American (Haarlem) T1;H1 RD182 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
gid 4407872 c.329_330delTG 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
gyrB 6127 c.888G>T synonymous_variant 0.13
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 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576113 p.Arg256Gly missense_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761034 p.Thr410Ala missense_variant 0.14
rpoC 764705 p.Leu446Met missense_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766507 p.Ile1046Met 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674352 p.Thr51Ser missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156040 c.72T>A synonymous_variant 0.14
PPE35 2169751 p.Gly288* stop_gained 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288999 p.Phe81Leu missense_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715580 c.-248G>A upstream_gene_variant 0.14
ahpC 2726759 c.567A>G synonymous_variant 0.11
folC 2747647 c.-49T>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449509 p.Glu336* stop_gained 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840291 c.1128_1129delTC frameshift_variant 0.11
alr 3840319 p.Pro368Ser missense_variant 0.12
alr 3841582 c.-162A>G upstream_gene_variant 0.11
alr 3841584 c.-164C>A upstream_gene_variant 0.11
alr 3841589 c.-170delG upstream_gene_variant 0.11
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 4248319 c.1806A>T synonymous_variant 0.2
embB 4249810 c.3297G>T stop_lost&splice_region_variant 0.29
aftB 4267263 c.1573delC frameshift_variant 0.11
ubiA 4269793 c.40delG frameshift_variant 0.11
ethR 4327402 c.-147C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0