TB-Profiler result

Run: ERR10748287
Summary

Run ID: ERR10748287

Sample name:

Date: 31-03-2023 10:49:57

Number of reads: 365423

Percentage reads mapped: 98.77

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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2289057 c.183_184dupAC frameshift_variant 0.91 pyrazinamide
ethR 4327831 p.Ala95Thr missense_variant 1.0 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
gyrB 7002 p.Asp588Ala missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8134 p.Val278Gly missense_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9730 p.Asp810Ala missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575455 c.108G>T synonymous_variant 0.4
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575949 p.Val201Gly missense_variant 0.18
ccsA 619844 c.-47T>G upstream_gene_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760591 p.Val262Gly missense_variant 0.17
rpoB 762457 p.Gly884Asp missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 763839 p.Val157Ala missense_variant 0.17
rpoC 764489 c.1120C>T synonymous_variant 0.4
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 766050 p.Glu894Ala missense_variant 0.22
rpoC 766981 c.3612T>G synonymous_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775653 p.Val943Gly missense_variant 0.43
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777293 c.1188T>G synonymous_variant 0.3
mmpR5 779327 p.Glu113Ala missense_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304011 p.Thr361Pro missense_variant 0.38
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406929 p.Ser138Ala missense_variant 0.43
Rv1258c 1407008 c.333C>A synonymous_variant 0.22
Rv1258c 1407045 p.Asp99Ala missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473580 n.-78G>T upstream_gene_variant 0.33
fabG1 1673558 p.His40Pro missense_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918035 c.96G>A synonymous_variant 0.25
tlyA 1918499 p.Val187Gly missense_variant 0.25
tlyA 1918524 c.585T>G synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168283 p.Asp777Ala missense_variant 0.22
PPE35 2170475 c.138C>A synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746584 p.Leu339Val missense_variant 0.38
folC 2746673 p.Val309Gly missense_variant 0.25
ribD 2986795 c.-44A>C upstream_gene_variant 0.3
ribD 2987396 c.558T>G synonymous_variant 0.22
thyX 3067405 p.Thr181Pro missense_variant 0.29
thyX 3068031 c.-86A>C upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087818 p.Cys333Trp missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474046 p.Ser14Ala missense_variant 0.29
fprA 3474306 c.300G>A synonymous_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613230 c.-114T>G upstream_gene_variant 0.5
fbiA 3640655 p.Asp38Ala missense_variant 0.5
fbiB 3642192 p.Phe220Leu missense_variant 0.23
fbiB 3642340 p.Asp269Ala missense_variant 0.25
fbiB 3642417 p.Thr295Pro missense_variant 0.25
rpoA 3877852 p.Phe219Cys missense_variant 0.33
ddn 3987207 p.Tyr122Asn missense_variant 0.33
clpC1 4038334 p.Phe791Leu missense_variant 0.4
clpC1 4040757 c.-53G>T upstream_gene_variant 0.18
panD 4044209 p.Ser25Ala missense_variant 0.4
embC 4240515 p.Val218Gly missense_variant 0.25
embA 4242472 c.-761G>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243689 p.Met153Leu missense_variant 0.25
embA 4244622 p.Ser464Ala missense_variant 0.29
embA 4245137 p.Tyr635* stop_gained 0.2
embA 4245789 p.Thr853Pro missense_variant 0.5
embA 4245835 p.Leu868Arg missense_variant 0.4
embB 4246527 p.Ala5Gly missense_variant 0.5
embB 4247033 p.Ser174Arg missense_variant 0.6
embB 4248690 p.Ile726Ser missense_variant 0.22
aftB 4267423 p.Thr472Pro missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267875 p.Leu321Arg missense_variant 0.5
aftB 4268498 c.339T>G synonymous_variant 0.5
ethR 4328003 p.Val152Glu missense_variant 0.18
ethA 4328225 c.-752A>C upstream_gene_variant 0.4
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