TB-Profiler result

Run: SRR6831995
Summary

Run ID: SRR6831995

Sample name:

Date: 04-04-2023 17:09:50

Number of reads: 1597439

Percentage reads mapped: 99.36

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.6 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288835 p.Asp136Gly missense_variant 0.36 pyrazinamide
pncA 2289100 p.Lys48Glu missense_variant 0.59 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.85 ethambutol
embB 4247469 p.Tyr319Cys missense_variant 0.29 ethambutol
ethA 4326589 c.884delT frameshift_variant 0.61 ethionamide, ethionamide
ethA 4327054 p.Tyr140* stop_gained 0.36 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
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761293 p.Val496Ala missense_variant 0.62
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766487 p.Pro1040Ser missense_variant 0.46
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.98
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746739 p.Ser287Tyr missense_variant 0.12
Rv2752c 3064899 c.1293G>T synonymous_variant 0.11
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612400 c.717G>A synonymous_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641852 c.318C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>T upstream_gene_variant 0.35
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243728 p.Lys166* stop_gained 0.13
embA 4245432 p.Ala734Thr missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267847 c.990C>T synonymous_variant 0.15
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0