TB-Profiler result

Run: ERR4972573
Summary

Run ID: ERR4972573

Sample name:

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

Number of reads: 467168

Percentage reads mapped: 19.03

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
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 9610 p.Asp770Val missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575314 c.-34C>A upstream_gene_variant 0.18
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.67
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761401 p.Arg532His missense_variant 0.17
rpoB 761455 p.Glu550Gly missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765408 c.2041delT frameshift_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776718 c.1762delG frameshift_variant 0.18
mmpL5 777793 p.Ala230Thr missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800734 c.-75C>A upstream_gene_variant 0.33
fbiC 1303212 c.282C>A synonymous_variant 0.11
Rv1258c 1406992 p.Gly117Arg missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472429 n.584T>A non_coding_transcript_exon_variant 0.4
inhA 1674247 p.Ile16Val missense_variant 0.17
rpsA 1834370 p.Lys277Glu missense_variant 0.29
rpsA 1834869 c.1329delC frameshift_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169751 p.Gly288* stop_gained 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519348 p.Ala412Thr missense_variant 0.17
pepQ 2860119 c.300C>T synonymous_variant 0.2
thyX 3067689 p.Ser86* stop_gained 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338950 c.-168C>T upstream_gene_variant 0.14
Rv3083 3448548 c.45C>A synonymous_variant 0.12
Rv3083 3449945 p.Gly481Ala missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.67
clpC1 4038494 c.2211G>A synonymous_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.17
embA 4242526 c.-707C>G upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244944 p.Ala571Val missense_variant 0.12
embA 4245817 p.Arg862His missense_variant 0.12
embB 4248049 c.1539delG frameshift_variant 0.1
embB 4248319 c.1806A>T synonymous_variant 0.3
embB 4248324 p.Ala604Gly missense_variant 0.22
ubiA 4269122 p.Phe238Val missense_variant 0.32
ethR 4327886 p.Thr113Arg missense_variant 0.13
whiB6 4338407 p.Asp39Asn missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408157 p.Leu16Val missense_variant 0.15
gid 4408309 c.-107A>G upstream_gene_variant 0.15