TB-Profiler result

Run: ERR11082441
Summary

Run ID: ERR11082441

Sample name:

Date: 10-04-2023 16:22:38

Number of reads: 5898321

Percentage reads mapped: 99.58

Strain: lineage4.3.3;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 0.57
lineage4 Euro-American LAM;T;S;X;H None 0.44
lineage4.3 Euro-American (LAM) mainly-LAM None 0.44
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.59
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.56
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.44
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 0.58 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288827 p.Val139Met missense_variant 0.46 pyrazinamide
pncA 2289054 p.Asp63Ala missense_variant 0.47 pyrazinamide
ddn 3987106 p.Trp88* stop_gained 0.52 delamanid
embB 4247574 p.Asp354Ala missense_variant 0.54 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.45 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.45
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.59
mshA 575472 p.Asp42Gly missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 0.57
ccsA 620625 p.Ile245Met missense_variant 0.52
rpoC 763031 c.-339T>C upstream_gene_variant 0.57
rpoC 764817 p.Val483Ala missense_variant 0.45
rpoC 764995 c.1626C>G synonymous_variant 0.4
rpoC 766667 p.Ser1100Ala missense_variant 0.46
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.55
mmpL5 776182 p.Asp767Asn missense_variant 0.68
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.53
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.59
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.57
PPE35 2167926 p.Leu896Ser missense_variant 0.56
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.44
thyA 3073868 p.Thr202Ala missense_variant 0.4
ald 3086731 c.-89A>G upstream_gene_variant 0.64
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339490 p.Leu125Ile missense_variant 0.44
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54
rpoA 3877956 p.Glu184Asp missense_variant 0.6
rpoA 3878630 c.-123G>C upstream_gene_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.58
embA 4243460 c.228C>T synonymous_variant 0.58
embA 4244823 p.Val531Leu missense_variant 0.37
embB 4248316 c.1803C>T synonymous_variant 0.47
aftB 4267647 p.Asp397Gly missense_variant 0.59
whiB6 4338371 p.Thr51Pro missense_variant 0.51
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.51
gid 4407927 p.Glu92Asp missense_variant 0.52
gid 4408009 p.Val65Ala missense_variant 0.41
gid 4408156 p.Leu16Arg missense_variant 0.42