TB-Profiler result

Run: ERR10748243
Summary

Run ID: ERR10748243

Sample name:

Date: 31-03-2023 10:48:41

Number of reads: 1177335

Percentage reads mapped: 99.86

Strain: lineage2.2.1.1;lineage1.2.2.1

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 0.42
lineage1 Indo-Oceanic EAI RD239 0.59
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.43
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.65
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.43
lineage1.2.2.1 Indo-Oceanic NA RD239 0.62
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.38
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 761139 p.His445Cys missense_variant 0.63 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.35 rifampicin
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
pncA 2289177 c.64delA frameshift_variant 0.52 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.8 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.73
gyrB 6112 p.Met291Ile missense_variant 0.62
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.61
gyrA 9143 c.1842T>C synonymous_variant 0.59
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 0.54
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.3
ccsA 620625 p.Ile245Met missense_variant 0.44
ccsA 620659 p.Arg257Cys missense_variant 0.57
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.54
rpoC 763886 c.517C>A synonymous_variant 0.57
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 0.39
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 0.57
Rv1258c 1406760 c.580_581insC frameshift_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 0.53
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.74
rpsA 1834177 c.636A>C synonymous_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101848 c.1195C>T synonymous_variant 0.53
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154977 p.Ala379Thr missense_variant 0.43
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 0.7
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.66
eis 2714846 p.Val163Ile missense_variant 0.26
ahpC 2726051 c.-142G>A upstream_gene_variant 0.66
ribD 2987120 c.282C>T synonymous_variant 0.7
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.71
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.62
fprA 3474938 p.Glu311Gly missense_variant 0.63
fprA 3475159 p.Asn385Asp missense_variant 0.52
Rv3236c 3612813 p.Thr102Ala missense_variant 0.31
clpC1 4040517 p.Val63Ala missense_variant 0.58
embC 4240671 p.Thr270Ile missense_variant 0.49
embC 4240750 c.888C>T synonymous_variant 0.67
embC 4241042 p.Asn394Asp missense_variant 0.62
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>T upstream_gene_variant 0.38
embA 4243460 c.228C>T synonymous_variant 0.39
embA 4245969 p.Pro913Ser missense_variant 0.61
embB 4247646 p.Glu378Ala missense_variant 0.73
embB 4248115 c.1602C>T synonymous_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 0.49
ubiA 4269387 p.Glu149Asp missense_variant 0.73
aftB 4269606 c.-770T>C upstream_gene_variant 0.67
ethA 4326439 p.Asn345Lys missense_variant 0.63
ethR 4327450 c.-99G>A upstream_gene_variant 0.63
ethA 4327602 c.-129C>T upstream_gene_variant 0.59
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.71
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.61
gid 4407927 p.Glu92Asp missense_variant 0.42