TB-Profiler result

Run: ERR8665570
Summary

Run ID: ERR8665570

Sample name:

Date: 02-04-2023 07:32:18

Number of reads: 568726

Percentage reads mapped: 99.54

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 2288836 p.Asp136Tyr missense_variant 0.23 pyrazinamide
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247729 p.Gly406Cys missense_variant 0.29 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 5721 p.Gly161Val missense_variant 0.15
gyrB 5934 p.Ser232* stop_gained 0.24
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9055 p.Pro585His missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491140 p.Gly120Cys missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575389 c.42C>A synonymous_variant 0.17
mshA 575787 p.Tyr147Cys missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576022 c.675T>C synonymous_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761049 c.1243C>A synonymous_variant 0.17
rpoB 761985 p.Asp727Tyr missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764875 c.1506C>A synonymous_variant 0.15
rpoC 764916 p.Leu516Pro missense_variant 1.0
rpoC 765280 c.1911G>T synonymous_variant 0.2
rpoC 765297 p.Pro643Leu missense_variant 0.18
rpoC 765738 p.Arg790Leu missense_variant 0.18
rpoC 765978 p.Ser870Tyr missense_variant 0.2
rpoC 766314 p.Ser982Tyr missense_variant 0.18
rpoC 766699 c.3330G>A synonymous_variant 0.12
rpoC 767080 c.3711G>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777204 p.Pro426Gln missense_variant 0.22
mmpL5 777215 c.1266C>A synonymous_variant 0.18
mmpL5 777220 p.Leu421Met missense_variant 0.18
mmpL5 777515 p.Phe322Leu missense_variant 0.22
mmpL5 777885 p.Ala199Asp missense_variant 0.15
mmpL5 778998 c.-518G>C upstream_gene_variant 0.14
mmpS5 779564 c.-659C>A upstream_gene_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303330 c.400C>A synonymous_variant 0.22
fbiC 1303554 c.624G>T synonymous_variant 0.33
fbiC 1303665 c.735G>T synonymous_variant 0.2
fbiC 1303899 c.969G>T synonymous_variant 0.2
fbiC 1304032 p.Glu368Lys missense_variant 0.33
fbiC 1304145 p.Trp405Cys missense_variant 0.33
fbiC 1304814 p.Met628Ile missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406968 p.Asp125Tyr missense_variant 0.2
Rv1258c 1407116 c.225G>T synonymous_variant 0.29
Rv1258c 1407169 p.Ala58Ser missense_variant 0.17
Rv1258c 1407365 c.-25G>T upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833977 p.Gly146Cys missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834294 c.753G>T synonymous_variant 0.15
rpsA 1834311 p.Glu257Val missense_variant 0.17
rpsA 1834717 p.Phe392Leu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918184 p.Ala82Val missense_variant 0.15
ndh 2101675 c.1368G>T synonymous_variant 0.2
ndh 2101683 p.Gly454Cys missense_variant 0.2
ndh 2102418 p.Ala209Ser missense_variant 0.14
ndh 2102875 p.Tyr56* stop_gained 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170571 p.Leu14Phe missense_variant 0.22
Rv1979c 2222688 c.477C>A synonymous_variant 0.25
Rv1979c 2223162 c.3G>T synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289011 c.231C>A synonymous_variant 0.2
pncA 2289327 c.-86C>G upstream_gene_variant 0.13
pncA 2289412 c.-171C>A upstream_gene_variant 0.18
pncA 2289444 c.-203T>C upstream_gene_variant 0.17
kasA 2518237 p.Ser41Arg missense_variant 0.14
kasA 2518599 p.Ala162Val missense_variant 0.13
kasA 2519185 c.1071C>A synonymous_variant 0.2
folC 2747418 p.Gln61Lys missense_variant 0.29
pepQ 2859776 p.Gly215Cys missense_variant 0.2
ribD 2987195 c.357C>A synonymous_variant 0.23
Rv2752c 3064619 p.Asp525Tyr missense_variant 0.25
thyX 3067391 c.555G>T synonymous_variant 0.22
thyX 3067762 p.Arg62Trp missense_variant 0.18
thyA 3074537 c.-66G>T upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339541 p.Asp142Tyr missense_variant 0.2
Rv3083 3448810 p.Lys103Glu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613037 p.Arg27Leu missense_variant 0.4
fbiA 3640465 c.-77delT upstream_gene_variant 0.11
fbiA 3640981 p.Asp147Tyr missense_variant 0.17
fbiB 3641639 c.105G>T synonymous_variant 0.25
fbiB 3641736 p.Glu68* stop_gained 0.2
fbiB 3642030 p.Gly166Cys missense_variant 0.33
alr 3840391 p.Asp344Tyr missense_variant 0.25
alr 3840552 p.Gly290Val missense_variant 0.14
alr 3840577 p.Ala282Ser missense_variant 0.14
alr 3841335 p.Ser29Tyr missense_variant 0.18
rpoA 3877569 c.939G>T synonymous_variant 0.23
ddn 3986742 c.-102G>T upstream_gene_variant 0.17
ddn 3987252 p.Gln137Lys missense_variant 0.17
clpC1 4038270 p.Pro812His missense_variant 0.17
clpC1 4039616 c.1089G>T synonymous_variant 0.18
clpC1 4040002 p.His235Asp missense_variant 0.18
clpC1 4040020 c.685C>T synonymous_variant 0.15
clpC1 4040135 c.570C>A synonymous_variant 0.25
panD 4043891 p.Leu131Met missense_variant 0.13
panD 4044032 p.Leu84Met missense_variant 0.18
embA 4242346 c.-887C>A upstream_gene_variant 0.17
embA 4242481 c.-752C>A upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244756 p.Glu508Asp missense_variant 0.15
embA 4245990 p.Pro920Ser missense_variant 0.17
embB 4246940 p.Pro143Thr missense_variant 0.22
embB 4247626 c.1113C>A synonymous_variant 0.14
embB 4247933 p.Gly474Cys missense_variant 0.17
embB 4248946 c.2433C>A synonymous_variant 0.18
embB 4249254 p.Gly914Val missense_variant 0.17
embB 4249502 p.Gln997Lys missense_variant 0.33
embB 4249660 p.Met1049Ile missense_variant 0.25
aftB 4267329 p.Arg503Gln missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267662 p.Ser392* stop_gained 0.25
aftB 4268338 p.Asp167Tyr missense_variant 0.22
ubiA 4269707 p.Gly43Cys missense_variant 0.17
ubiA 4269761 p.Gln25Lys missense_variant 0.18
ubiA 4269990 c.-157G>T upstream_gene_variant 0.33
ethA 4326127 p.Gln449His missense_variant 0.18
ethA 4326881 p.Gly198Val missense_variant 0.13
ethA 4327131 p.Arg115Gly missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407537 c.666G>T synonymous_variant 0.25
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408173 c.30G>T synonymous_variant 0.25
gid 4408190 p.Glu5* stop_gained 0.33