TB-Profiler result

Run: SRR6256988
Summary

Run ID: SRR6256988

Sample name:

Date: 04-04-2023 13:21:58

Number of reads: 893774

Percentage reads mapped: 100.0

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
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
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 8543 c.1242C>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 0.96
fgd1 490994 p.Gly71Asp missense_variant 0.12
fgd1 491099 p.Gly106Asp missense_variant 0.14
fgd1 491108 p.Glu109Gly missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575210 c.-138C>A upstream_gene_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576139 c.792C>T synonymous_variant 0.17
mshA 576664 c.1317C>A synonymous_variant 0.25
ccsA 620461 p.Val191Phe missense_variant 0.29
ccsA 620551 p.Asp221His missense_variant 0.22
ccsA 620564 p.Leu225Pro missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620651 p.Ala254Asp missense_variant 0.13
ccsA 620772 p.Trp294Cys missense_variant 0.2
rpoB 761123 c.1317G>C synonymous_variant 0.12
rpoB 761790 p.Arg662Ser missense_variant 0.12
rpoB 762269 p.Glu821Asp missense_variant 0.29
rpoB 762312 p.Gly836Cys missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764138 p.Gly257Cys missense_variant 0.13
rpoC 764263 c.894G>T synonymous_variant 0.13
rpoC 764925 p.Gly519Asp missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
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 777279 p.Ala401Glu missense_variant 0.33
mmpL5 777837 p.Ile215Asn missense_variant 0.12
mmpR5 779261 p.Thr91Ser missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304067 c.1137G>T synonymous_variant 0.17
fbiC 1304202 c.1272G>T synonymous_variant 0.12
Rv1258c 1406265 p.Ala359Asp missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407153 p.Gly63Ala missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674151 p.Pro238Thr missense_variant 0.15
fabG1 1674182 c.743G>C stop_lost&splice_region_variant 0.11
inhA 1674963 c.762G>T synonymous_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918263 c.324G>T synonymous_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170436 c.177T>C synonymous_variant 0.17
PPE35 2170617 c.-5G>C upstream_gene_variant 0.12
PPE35 2170628 c.-16C>T upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714222 p.Ala371Ser missense_variant 0.18
eis 2714291 p.Glu348* stop_gained 0.17
eis 2714310 c.1023C>A synonymous_variant 0.14
eis 2714488 p.Thr282Asn missense_variant 0.13
eis 2714500 p.Leu278Arg missense_variant 0.13
eis 2715514 c.-182C>T upstream_gene_variant 0.14
ahpC 2726102 c.-91T>C upstream_gene_variant 0.1
folC 2746267 c.1332C>G synonymous_variant 0.12
folC 2746590 p.Gly337Cys missense_variant 0.18
pepQ 2859660 c.759G>T synonymous_variant 0.14
pepQ 2860185 c.234G>C synonymous_variant 0.11
ribD 2986745 c.-94C>T upstream_gene_variant 0.13
ribD 2987475 p.Leu213Val missense_variant 0.11
Rv2752c 3066132 c.60G>C synonymous_variant 0.11
Rv2752c 3067186 c.-995G>T upstream_gene_variant 0.12
thyX 3068064 c.-119G>C upstream_gene_variant 0.12
thyA 3073715 p.Pro253Ala missense_variant 1.0
thyA 3074502 c.-31C>G upstream_gene_variant 0.11
thyA 3074602 c.-131G>T upstream_gene_variant 0.12
thyA 3074614 c.-143G>C upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087230 c.411C>A synonymous_variant 0.14
ald 3087286 p.Arg156Leu missense_variant 0.12
ald 3087416 c.597C>A synonymous_variant 0.14
ald 3087880 p.Arg354Leu missense_variant 0.13
ald 3087887 c.1068C>A synonymous_variant 0.25
fbiD 3339078 c.-40C>A upstream_gene_variant 0.18
fbiD 3339232 p.Val39Leu missense_variant 0.14
fbiD 3339739 p.Ala208Pro missense_variant 0.11
Rv3083 3448967 p.Gly155Val missense_variant 0.12
Rv3083 3449057 p.Ser185Ile missense_variant 0.12
Rv3083 3449084 p.Pro194Arg missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474664 p.Gly220Trp missense_variant 0.17
Rv3236c 3612716 p.Ala134Gly missense_variant 0.15
Rv3236c 3612752 p.Ala122Asp missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612858 p.Arg87Gly missense_variant 0.1
fbiB 3642108 p.Val192Leu missense_variant 0.13
fbiB 3642782 c.1248C>A synonymous_variant 0.14
alr 3840296 c.1125G>C synonymous_variant 0.11
alr 3841111 p.Gly104Cys missense_variant 0.14
rpoA 3878536 c.-29G>T upstream_gene_variant 0.15
rpoA 3878593 c.-86C>A upstream_gene_variant 0.25
rpoA 3878601 c.-94C>A upstream_gene_variant 0.18
clpC1 4038171 p.Pro845Gln missense_variant 0.3
clpC1 4038242 c.2463C>A synonymous_variant 0.17
clpC1 4038258 p.Ala816Glu missense_variant 0.15
clpC1 4039777 p.Pro310Ser missense_variant 0.14
clpC1 4040198 p.Leu169Phe missense_variant 0.12
panD 4044422 c.-141C>A upstream_gene_variant 0.13
embC 4240517 p.Asp219His missense_variant 0.17
embA 4242373 c.-860C>A upstream_gene_variant 0.15
embA 4242478 c.-755C>A upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242773 p.Leu971Met missense_variant 0.17
embA 4243048 c.-185G>T upstream_gene_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243896 p.Ala222Ser missense_variant 0.12
embA 4244150 p.Trp306Cys missense_variant 0.12
embA 4244393 c.1161G>C synonymous_variant 0.11
embA 4244421 p.Glu397* stop_gained 0.15
embA 4244438 c.1206C>A synonymous_variant 0.22
embA 4244515 p.Ala428Val missense_variant 0.17
embA 4244963 p.Phe577Leu missense_variant 0.17
embB 4247096 p.Pro195Ser missense_variant 0.14
embB 4247758 c.1245C>G synonymous_variant 0.11
embB 4247886 p.Gly458Val missense_variant 0.14
embB 4247930 p.Val473Phe missense_variant 0.12
embB 4248300 p.Phe596Ser missense_variant 0.13
embB 4248605 p.Leu698Met missense_variant 0.18
embB 4248636 p.Pro708Gln missense_variant 0.2
embB 4249221 p.Ala903Val missense_variant 0.14
embB 4249227 p.Pro905Gln missense_variant 0.17
embB 4249333 c.2821delG frameshift_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269073 p.Pro254Arg missense_variant 0.1
ethA 4326533 p.Thr314Ile missense_variant 1.0
ethR 4327703 p.Lys52Arg missense_variant 0.11
ethR 4328086 p.Glu180Gln missense_variant 0.11
whiB6 4338232 p.Ser97Tyr missense_variant 0.15
whiB6 4338458 p.Thr22Ala missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338653 c.-132G>T upstream_gene_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408334 c.-132G>T upstream_gene_variant 0.13