TB-Profiler result

Run: ERR4195457
Summary

Run ID: ERR4195457

Sample name:

Date: 01-04-2023 05:18:26

Number of reads: 1008268

Percentage reads mapped: 97.36

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 0.99
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575458 c.111T>C synonymous_variant 0.18
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619725 c.-166C>T upstream_gene_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764363 p.Gly332Cys missense_variant 1.0
rpoC 765341 p.Pro658Ser missense_variant 0.18
rpoC 767041 c.3672G>T synonymous_variant 0.12
rpoC 767263 c.3895delG frameshift_variant 0.13
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
fbiC 1303932 c.1002G>T synonymous_variant 0.14
fbiC 1304264 p.Gly445Asp missense_variant 0.12
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 1.0
rpsA 1834872 p.Gly444Val missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918590 c.651G>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169984 p.Ala210Val missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289082 p.Pro54Ala missense_variant 1.0
pncA 2289894 c.-653G>A upstream_gene_variant 0.17
eis 2715432 c.-100C>T upstream_gene_variant 0.12
eis 2715436 c.-104G>A upstream_gene_variant 0.12
eis 2715440 c.-108A>C upstream_gene_variant 0.11
eis 2715450 c.-118T>C upstream_gene_variant 0.12
eis 2715451 c.-119C>A upstream_gene_variant 0.12
eis 2715454 c.-122T>G upstream_gene_variant 0.12
eis 2715455 c.-123G>A upstream_gene_variant 0.12
eis 2715458 c.-126T>A upstream_gene_variant 0.12
eis 2715460 c.-128A>G upstream_gene_variant 0.12
eis 2715465 c.-133G>T upstream_gene_variant 0.12
eis 2715469 c.-137T>C upstream_gene_variant 0.12
eis 2715473 c.-141A>G upstream_gene_variant 0.12
pepQ 2859615 c.804C>A synonymous_variant 0.33
pepQ 2859992 p.Leu143Val missense_variant 0.12
pepQ 2860248 c.171C>T synonymous_variant 0.11
Rv2752c 3065678 p.Lys172Glu missense_variant 1.0
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 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612873 p.Phe82Ile missense_variant 0.11
fbiB 3642083 p.Tyr183* stop_gained 0.11
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243702 c.473_489delGCGCCGGGACCCTGCCG frameshift_variant 0.11
embA 4245943 p.Arg904His missense_variant 0.11
embB 4246719 p.Ala69Asp missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269355 p.Arg160Leu missense_variant 0.12
ethA 4326713 p.Gln254Pro missense_variant 1.0
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