TB-Profiler result

Run: SRR3085346
Summary

Run ID: SRR3085346

Sample name:

Date: 04-04-2023 04:59:15

Number of reads: 462032

Percentage reads mapped: 99.43

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 0.99
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 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747480 p.Glu40Gly missense_variant 1.0 para-aminosalicylic_acid
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 5244 p.Ala2Val missense_variant 0.14
gyrA 6604 c.-698G>A upstream_gene_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760466 c.660C>T synonymous_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_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
mmpS5 779615 c.-710C>G upstream_gene_variant 0.86
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801330 c.522G>A synonymous_variant 0.12
fbiC 1304891 p.Ile654Thr missense_variant 0.17
fbiC 1304894 p.Gly655Val missense_variant 0.2
Rv1258c 1406519 c.822A>T synonymous_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918609 p.Gly224Ser missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222777 p.Ala130Thr missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519214 c.1103delC frameshift_variant 0.33
eis 2714610 c.723C>T synonymous_variant 0.2
thyA 3074503 c.-32G>C upstream_gene_variant 0.62
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473968 c.-39C>T upstream_gene_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613070 p.Ala16Val missense_variant 0.29
fbiB 3641718 p.Pro62Ser missense_variant 0.2
fbiB 3642396 c.866delC frameshift_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244132 c.900G>C synonymous_variant 0.18
embA 4244141 c.909G>T synonymous_variant 0.14
embB 4247367 p.Phe285Ser missense_variant 0.13
embB 4249133 c.2620C>T synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.93