TB-Profiler result

Run: ERR8665568

Summary

Run ID: ERR8665568

Sample name:

Date: 02-04-2023 07:32:13

Number of reads: 579651

Percentage reads mapped: 99.56

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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
pncA 2289097 p.Asp49Tyr missense_variant 0.18 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
ethA 4326166 c.1307dupC frameshift_variant 1.0 ethionamide, 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
gyrB 6290 p.Arg351Gly missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7409 c.108C>A synonymous_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491528 p.Trp249Leu missense_variant 0.17
fgd1 491634 p.Trp284Cys missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576473 p.Gly376Trp missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759703 c.-104C>T upstream_gene_variant 0.23
rpoB 760614 p.Asp270Tyr missense_variant 0.18
rpoB 761315 p.Phe503Leu missense_variant 0.2
rpoB 761453 c.1647C>A synonymous_variant 0.19
rpoB 761471 c.1665C>A synonymous_variant 0.2
rpoB 762150 p.Gly782Cys missense_variant 0.14
rpoB 762620 p.Trp938Cys missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763732 c.363C>A synonymous_variant 0.17
rpoC 763800 p.Arg144Leu missense_variant 0.29
rpoC 764741 p.Lys458Glu missense_variant 0.14
rpoC 764916 p.Leu516Pro missense_variant 1.0
rpoC 765388 p.Phe673Leu missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775706 p.Met925Ile missense_variant 0.29
mmpL5 776002 p.Leu827Met missense_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776219 c.2262C>A synonymous_variant 0.29
mmpL5 776552 p.Gln643His missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781459 c.-101G>T upstream_gene_variant 0.2
fbiC 1302961 p.Ala11Ser missense_variant 0.14
fbiC 1304173 p.Val415Leu missense_variant 0.22
fbiC 1304443 p.Ala505Ser missense_variant 0.33
fbiC 1304449 p.Ala507Ser missense_variant 0.33
fbiC 1305351 c.2421G>T synonymous_variant 0.17
Rv1258c 1406300 c.1041G>T synonymous_variant 0.17
Rv1258c 1406752 p.Gly197Cys missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407068 c.273G>T synonymous_variant 0.17
Rv1258c 1407143 c.198C>A synonymous_variant 0.22
embR 1416268 c.1080G>T synonymous_variant 0.18
embR 1416484 c.864G>T synonymous_variant 0.2
embR 1416636 p.Asp238Tyr missense_variant 0.18
embR 1416828 p.His174Asn missense_variant 0.3
embR 1416997 c.351C>A synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834714 c.1173C>A synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101828 c.1215C>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155256 p.Pro286Thr missense_variant 0.15
katG 2156551 c.-440C>T upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169109 p.Asp502Tyr missense_variant 0.29
PPE35 2170267 p.Gly116Cys missense_variant 0.22
Rv1979c 2222322 p.Lys281Asn missense_variant 0.18
Rv1979c 2222329 p.Ser279Leu missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290190 c.-949C>A upstream_gene_variant 0.22
kasA 2518960 c.846C>A synonymous_variant 0.15
folC 2746639 p.Gln320His missense_variant 0.14
folC 2746752 p.Gly283Cys missense_variant 0.67
folC 2747033 p.Ala189Glu missense_variant 0.17
folC 2747206 c.393G>T synonymous_variant 0.29
pepQ 2859330 c.1089C>A synonymous_variant 0.13
pepQ 2860193 p.Glu76* stop_gained 0.25
ribD 2987034 p.Gly66Cys missense_variant 0.18
ribD 2987279 c.441G>T synonymous_variant 0.18
ribD 2987573 c.735C>A synonymous_variant 0.2
Rv2752c 3064806 c.1386G>T synonymous_variant 0.2
Rv2752c 3065316 c.876C>A synonymous_variant 0.18
Rv2752c 3065335 p.Leu286Pro missense_variant 0.2
Rv2752c 3065952 c.240C>A synonymous_variant 0.14
Rv2752c 3066269 c.-78A>G upstream_gene_variant 0.18
thyX 3067322 c.624C>A synonymous_variant 0.25
thyX 3067342 p.Glu202* stop_gained 0.25
thyX 3067576 p.Asp124Tyr missense_variant 0.18
thyA 3073920 c.552C>A synonymous_variant 0.18
thyA 3074331 c.141C>A synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086890 p.Ala24Glu missense_variant 0.2
ald 3087823 p.Ser335* stop_gained 0.18
Rv3083 3448578 c.75C>A synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474787 p.Arg261Cys missense_variant 0.17
fprA 3474895 p.Asp297Tyr missense_variant 0.22
fprA 3474968 p.Ser321* stop_gained 0.18
Rv3236c 3612275 p.Ser281* stop_gained 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642596 c.1062C>A synonymous_variant 0.17
alr 3841084 c.337C>T synonymous_variant 0.22
alr 3841552 c.-132C>A upstream_gene_variant 0.17
rpoA 3878644 c.-137G>C upstream_gene_variant 0.17
clpC1 4038176 c.2529G>T synonymous_variant 0.18
clpC1 4038577 p.Leu710Ile missense_variant 0.2
clpC1 4039640 c.1065C>A synonymous_variant 0.25
panD 4044417 c.-136C>A upstream_gene_variant 0.43
embC 4239880 c.18C>A synonymous_variant 0.2
embC 4240015 c.153G>T synonymous_variant 0.15
embC 4240559 p.Ala233Thr missense_variant 0.14
embC 4242007 c.2145G>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242693 p.Arg944Leu missense_variant 0.3
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243661 c.429C>A synonymous_variant 0.22
embA 4243716 p.Leu162Met missense_variant 0.18
embA 4244510 p.Leu426Phe missense_variant 0.4
embA 4245512 c.2280G>T synonymous_variant 0.2
embA 4245540 p.Val770Phe missense_variant 0.2
embA 4245991 p.Pro920His missense_variant 0.18
embA 4246387 p.Arg1052Leu missense_variant 0.14
embB 4247737 c.1224C>A synonymous_variant 0.22
embB 4247743 c.1230C>A synonymous_variant 0.25
embB 4248991 c.2478C>A synonymous_variant 0.18
embB 4249185 p.Gly891Val missense_variant 0.23
aftB 4267107 p.Ser577Tyr missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268051 c.786G>T synonymous_variant 0.15
aftB 4268807 c.30G>T synonymous_variant 0.29
ethA 4327392 p.Pro28Thr missense_variant 0.15
ethA 4328091 c.-618C>A upstream_gene_variant 0.17
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