TB-Profiler result

Run: ERR11068679
Summary

Run ID: ERR11068679

Sample name:

Date: 06-04-2023 21:51:13

Number of reads: 3700681

Percentage reads mapped: 99.5

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 0.99
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289100 p.Lys48Glu missense_variant 0.64 pyrazinamide
pncA 2289171 p.Gly24Asp missense_variant 0.47 pyrazinamide
eis 2715339 c.-8delC upstream_gene_variant 0.33 kanamycin
folC 2747480 p.Glu40Gly missense_variant 0.33 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.62 ethambutol
ethA 4327033 p.Tyr147* stop_gained 0.68 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
mshA 576113 p.Arg256Gly missense_variant 0.33
mshA 576119 p.Ala258Pro missense_variant 0.29
mshA 576508 c.1161C>T synonymous_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763934 p.Ala189Thr missense_variant 0.13
rpoC 764840 p.Ile491Val missense_variant 0.69
rpoC 764918 p.Val517Leu missense_variant 0.37
rpoC 766645 p.Glu1092Asp missense_variant 0.53
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 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416973 c.375G>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155738 p.Gly125Asp missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169417 p.Thr399Arg missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746334 p.Gly422Asp missense_variant 0.29
ald 3086731 c.-89A>G upstream_gene_variant 0.35
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339745 p.Ala210Thr missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474963 c.957G>T synonymous_variant 0.14
fprA 3475297 p.Arg431Trp missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>A upstream_gene_variant 0.75
embA 4243346 c.114A>G synonymous_variant 0.33
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243995 p.Ala255Thr missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326855 p.Arg207Cys missense_variant 0.46
ethR 4327988 p.Ala147Gly missense_variant 0.11
ethA 4328025 c.-552T>C upstream_gene_variant 0.25
whiB6 4338371 p.Thr51Pro missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.99