TB-Profiler result

Run: ERR4553749

Summary

Run ID: ERR4553749

Sample name:

Date: 01-04-2023 06:19:34

Number of reads: 1662369

Percentage reads mapped: 99.55

Strain:

Drug-resistance: MDR-TB


Download CSV Download TXT Download PDF Download JSON
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
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.96
lineage1.1.3.1 Indo-Oceanic NA RD239 0.95
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 761095 p.Leu430Pro missense_variant 0.98 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.67 isoniazid, ethionamide
pncA 2289119 p.Tyr41* stop_gained 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.91 ethambutol
ethA 4327054 p.Tyr140* stop_gained 0.96 ethionamide
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 5117 c.-123G>A upstream_gene_variant 0.5
gyrB 6112 p.Met291Ile missense_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.97
gyrA 9143 c.1842T>C synonymous_variant 0.75
gyrA 9304 p.Gly668Asp missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.34
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 765171 p.Pro601Leu missense_variant 0.5
rpoC 765230 p.Ala621Thr missense_variant 0.79
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 0.96
mmpR5 779120 p.Leu44Pro missense_variant 0.98
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
ndh 2102054 p.Pro330Leu missense_variant 0.93
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169269 p.Gln448His missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222534 p.Ala211Thr missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 0.96
fbiD 3339734 p.Ala206Gly missense_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.94
fprA 3475159 p.Asn385Asp missense_variant 0.5
whiB7 3568425 c.255T>G synonymous_variant 0.17
alr 3841253 c.168C>T synonymous_variant 0.84
alr 3841277 c.144C>T synonymous_variant 0.85
embC 4240671 p.Thr270Ile missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.98
embB 4246584 p.Arg24Pro missense_variant 0.47
embB 4247646 p.Glu378Ala missense_variant 0.69
ubiA 4269387 p.Glu149Asp missense_variant 0.86
aftB 4269606 c.-770T>C upstream_gene_variant 0.91
whiB6 4338431 p.Leu31Val missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.9
gid 4407780 c.423G>A synonymous_variant 0.87
gid 4407873 c.330G>T synonymous_variant 0.86
gid 4408098 c.104dupT frameshift_variant 0.97
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0