TB-Profiler result

Run: ERR1194808
Summary

Run ID: ERR1194808

Sample name:

Date: 31-03-2023 12:34:19

Number of reads: 750307

Percentage reads mapped: 99.47

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 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.84 isoniazid, 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
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 491489 p.Asp236Ala missense_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.21
mshA 576490 c.1143G>C synonymous_variant 0.1
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761496 p.Tyr564Asp missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764466 p.Ile366Asn missense_variant 0.2
rpoC 764543 p.Thr392Ala missense_variant 0.18
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 777297 p.Val395Gly missense_variant 0.18
mmpL5 777963 p.Val173Gly missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303601 p.Glu224Val missense_variant 0.12
Rv1258c 1406730 p.Arg204Pro missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473577 n.-81A>T upstream_gene_variant 0.25
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917761 c.-179C>A upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168033 c.2580C>A synonymous_variant 0.22
PPE35 2169063 p.Met517Lys missense_variant 0.22
PPE35 2170131 p.Val161Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290174 c.-933A>G upstream_gene_variant 0.29
kasA 2519097 p.Val328Gly missense_variant 0.3
eis 2714905 p.Asp143Ala missense_variant 0.11
ahpC 2726657 c.465A>C synonymous_variant 0.15
folC 2746580 p.Glu340Gly missense_variant 0.33
folC 2747036 p.Asn188Thr missense_variant 0.18
Rv2752c 3065500 p.Gly231Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642216 p.Thr228Pro missense_variant 0.22
rpoA 3878490 c.18C>G synonymous_variant 0.5
clpC1 4038546 p.His720Pro missense_variant 0.29
clpC1 4038894 p.Tyr604Phe missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248689 p.Ile726Val missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268619 p.Val73Gly missense_variant 0.25
ubiA 4269304 p.Leu177* stop_gained 0.2
ubiA 4269964 c.-131T>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407712 p.Gly164Asp missense_variant 0.15
gid 4407927 p.Glu92Asp missense_variant 1.0