TB-Profiler result

Run: SRR998855
Summary

Run ID: SRR998855

Sample name:

Date: 04-04-2023 23:38:59

Number of reads: 1269342

Percentage reads mapped: 93.78

Strain: lineage4.3.3;lineage2.2.1

Drug-resistance: Sensitive

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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 0.62
lineage4 Euro-American LAM;T;S;X;H None 0.46
lineage4.3 Euro-American (LAM) mainly-LAM None 0.41
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.61
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.53
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.47
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
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 8040 p.Gly247Ser missense_variant 0.28
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.52
mshA 575907 p.Ala187Val missense_variant 0.52
ccsA 620625 p.Ile245Met missense_variant 0.7
rpoC 763031 c.-339T>C upstream_gene_variant 0.66
rpoC 764995 c.1626C>G synonymous_variant 0.48
rpoC 766645 p.Glu1092Asp missense_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.5
mmpL5 776182 p.Asp767Asn missense_variant 0.47
mmpL5 777119 p.His454Gln missense_variant 0.17
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.16
mmpS5 779615 c.-710C>G upstream_gene_variant 0.68
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.52
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.49
rpsA 1834836 p.Met432Thr missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.52
katG 2156196 c.-85C>T upstream_gene_variant 0.32
PPE35 2167926 p.Leu896Ser missense_variant 0.52
PPE35 2169269 c.1344A>G synonymous_variant 0.11
PPE35 2169272 c.1341C>G synonymous_variant 0.11
PPE35 2169278 c.1335T>C synonymous_variant 0.11
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169287 c.1326T>C synonymous_variant 0.2
PPE35 2169988 p.Leu209Met missense_variant 0.11
PPE35 2170363 p.Glu84Gln missense_variant 0.13
PPE35 2170372 p.Thr81Ala missense_variant 0.13
PPE35 2170623 c.-11G>A upstream_gene_variant 0.47
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.11
kasA 2518919 p.Gly269Ser missense_variant 0.32
kasA 2519128 c.1014G>C synonymous_variant 0.15
kasA 2519131 c.1017G>C synonymous_variant 0.15
kasA 2519140 c.1026G>C synonymous_variant 0.32
kasA 2519143 c.1029G>C synonymous_variant 0.28
eis 2714955 c.378C>T synonymous_variant 0.56
folC 2746340 p.Ala420Val missense_variant 0.32
thyA 3073868 p.Thr202Ala missense_variant 0.41
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339630 c.513C>T synonymous_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.81
clpC1 4038287 c.2418C>T synonymous_variant 0.5
clpC1 4038968 c.1737G>A synonymous_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.13
embA 4243157 c.-76G>C upstream_gene_variant 0.61
embA 4243460 c.228C>T synonymous_variant 0.52
aftB 4267647 p.Asp397Gly missense_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.47
gid 4407927 p.Glu92Asp missense_variant 0.54
gid 4408156 p.Leu16Arg missense_variant 0.3