TB-Profiler result

Run: SRR11972260
Summary

Run ID: SRR11972260

Sample name:

Date: 03-04-2023 05:33:54

Number of reads: 482500

Percentage reads mapped: 99.2

Strain: lineage2.2.1

Drug-resistance: HR-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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288933 p.Tyr103* stop_gained 0.12 pyrazinamide
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 7962 p.Gly221Trp missense_variant 0.13
gyrA 9301 p.Ala667Val missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491086 p.Phe102Leu missense_variant 0.12
fgd1 491439 c.657C>T synonymous_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620048 p.Ser53Leu missense_variant 0.13
ccsA 620455 p.Ala189Thr missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759721 c.-86G>T upstream_gene_variant 0.15
rpoB 759888 p.Gly28Arg missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764311 c.942C>T synonymous_variant 0.12
rpoC 764745 p.Arg459Gln missense_variant 0.22
rpoC 765182 p.Asp605Tyr missense_variant 0.18
rpoC 765254 p.Val629Met missense_variant 0.25
rpoC 765754 c.2385C>T synonymous_variant 0.17
rpoC 766034 p.His889Tyr missense_variant 0.12
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 777015 p.Gly489Val missense_variant 0.15
mmpL5 778950 c.-470C>T upstream_gene_variant 0.25
mmpR5 779297 p.Gly103Asp missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407075 p.Val89Ala missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
inhA 1674366 c.165G>C synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917898 c.-42T>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918381 p.Val148Ile missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155490 p.Glu208Lys missense_variant 0.14
PPE35 2167923 p.Gly897Asp missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168302 p.Thr771Ala missense_variant 0.15
PPE35 2170362 p.Glu84Val missense_variant 0.18
PPE35 2170392 p.Gly74Ala missense_variant 0.17
PPE35 2170400 c.213G>C synonymous_variant 0.14
Rv1979c 2222333 p.Gly278* stop_gained 0.17
Rv1979c 2222451 c.714C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223332 c.-168A>G upstream_gene_variant 0.12
Rv1979c 2223363 c.-199A>G upstream_gene_variant 0.12
ahpC 2726255 c.63T>G synonymous_variant 0.11
folC 2746785 p.Val272Ile missense_variant 0.21
folC 2747046 p.Asn185Asp missense_variant 0.15
folC 2747444 p.Ala52Val missense_variant 0.2
ribD 2986994 c.156C>T synonymous_variant 0.15
Rv2752c 3065225 p.His323Tyr missense_variant 0.2
thyX 3068049 c.-104C>T upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612334 p.Met261Ile missense_variant 0.12
Rv3236c 3612392 p.Val242Ala missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642459 p.Leu309Met missense_variant 1.0
alr 3841067 c.354C>T synonymous_variant 0.13
alr 3841406 p.Trp5* stop_gained 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.17
clpC1 4038773 p.Asp644Glu missense_variant 0.17
clpC1 4038776 p.Glu643Asp missense_variant 0.15
clpC1 4038788 c.1917G>A synonymous_variant 0.17
clpC1 4039177 p.Met510Val missense_variant 0.2
clpC1 4039645 p.His354Asp missense_variant 0.38
clpC1 4039743 p.Gly321Asp missense_variant 0.17
clpC1 4039829 p.Leu292Ile missense_variant 0.12
clpC1 4039838 c.867G>A synonymous_variant 0.14
embC 4240650 p.Leu263Arg missense_variant 0.14
embC 4241780 p.Trp640Arg missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243009 c.-224C>T upstream_gene_variant 0.17
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243940 p.Trp236* stop_gained 0.13
embB 4246094 c.-420C>T upstream_gene_variant 0.13
embB 4246340 c.-174G>A upstream_gene_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326878 p.Ala199Val missense_variant 0.12
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