TB-Profiler result

Run: ERR4830535
Summary

Run ID: ERR4830535

Sample name:

Date: 01-04-2023 20:16:41

Number of reads: 434043

Percentage reads mapped: 99.66

Strain: lineage4.8.1

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
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288790 p.Leu151Ser missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Asp 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 8927 p.Lys542Asn missense_variant 0.11
mshA 575742 p.Phe132Tyr missense_variant 0.12
rpoB 761159 c.1353G>A synonymous_variant 0.11
rpoB 761596 p.Asn597Ile missense_variant 0.17
rpoB 761961 p.Pro719Thr missense_variant 0.12
rpoC 765144 c.1779delC frameshift_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776081 c.2400G>A synonymous_variant 0.15
mmpL5 777765 p.Gly239Glu missense_variant 0.11
mmpS5 779489 c.-584C>T upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406819 p.Met174Ile missense_variant 0.13
Rv1258c 1406894 c.447C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475820 n.2163C>T non_coding_transcript_exon_variant 0.11
inhA 1674416 p.Ala72Val missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102547 p.Arg166Trp missense_variant 0.13
ndh 2102576 p.Glu156Gly missense_variant 0.11
PPE35 2167899 p.Gly905Val missense_variant 0.1
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170765 c.-153G>A upstream_gene_variant 0.17
PPE35 2170766 c.-154T>C upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289814 c.-573G>T upstream_gene_variant 0.15
pncA 2290051 c.-810C>A upstream_gene_variant 0.12
kasA 2518348 c.234A>T synonymous_variant 0.11
kasA 2518504 c.390T>C synonymous_variant 0.29
ahpC 2726612 c.420C>A synonymous_variant 0.11
folC 2747324 p.Arg92His missense_variant 0.14
pepQ 2859825 c.594C>T synonymous_variant 0.15
pepQ 2860078 p.Leu114Pro missense_variant 0.15
pepQ 2860378 c.40delA frameshift_variant 0.1
thyA 3074523 c.-52G>A upstream_gene_variant 0.11
ald 3087055 p.Ala79Glu missense_variant 0.1
ald 3087472 p.Arg218Leu missense_variant 0.13
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
fprA 3474404 p.Asn133Ile missense_variant 0.15
fprA 3474667 p.Val221Ile missense_variant 0.11
whiB7 3568567 p.Val38Ala missense_variant 0.11
fbiB 3641740 p.Gln69Leu missense_variant 0.14
fbiB 3642215 c.681G>T synonymous_variant 0.2
fbiB 3642567 p.Pro345Ser missense_variant 0.2
fbiB 3642874 p.Leu447Arg missense_variant 1.0
alr 3840337 p.Glu362Lys missense_variant 0.12
alr 3841511 c.-91C>A upstream_gene_variant 0.11
ddn 3987067 p.Val75Asp missense_variant 0.11
ddn 3987160 p.Val106Ala missense_variant 0.12
clpC1 4038922 p.Phe595Leu missense_variant 0.13
embC 4240147 c.285C>A synonymous_variant 0.12
embC 4241770 p.Ser636Arg missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243336 p.Pro35Gln missense_variant 0.13
embA 4243386 p.Asp52Tyr missense_variant 0.17
embA 4243952 p.Tyr240* stop_gained 0.12
embB 4245692 c.-822G>A upstream_gene_variant 0.29
embB 4248314 p.Ala601Pro missense_variant 0.1
aftB 4267892 c.945C>T synonymous_variant 0.29
ethA 4327243 p.Asp77Glu missense_variant 0.11
ethR 4327571 p.Gln8Leu missense_variant 0.15
ethA 4328396 c.-923C>A upstream_gene_variant 0.15
ethA 4328436 c.-963G>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0