TB-Profiler result

Run: ERR4553739
Summary

Run ID: ERR4553739

Sample name:

Date: 01-04-2023 06:19:13

Number of reads: 1186682

Percentage reads mapped: 99.54

Strain:

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
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 761161 p.Leu452Pro missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289058 p.Pro62Ser missense_variant 0.28 pyrazinamide
pncA 2289142 p.Tyr34Asp missense_variant 0.11 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 0.13 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.69 ethambutol
gid 4408100 c.102delG 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 8452 p.Ala384Val missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765312 p.Ala648Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169041 c.1572G>A synonymous_variant 1.0
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169059 c.1554G>A synonymous_variant 1.0
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Thr missense_variant 1.0
PPE35 2169068 c.1545G>T synonymous_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222641 p.Ser175Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
folC 2746488 p.Asp371Tyr missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448721 p.Lys73Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243245 p.Gly5Arg missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244148 p.Trp306Arg missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.13
embB 4248946 c.2433C>T synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326953 p.Asp174Gly missense_variant 1.0
whiB6 4338289 p.Gly78Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0