TB-Profiler result

Run: SRR6256994
Summary

Run ID: SRR6256994

Sample name:

Date: 04-04-2023 13:22:15

Number of reads: 634908

Percentage reads mapped: 99.67

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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155192 p.Gly307Glu missense_variant 0.1 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247399 p.Asn296His missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide, ethionamide
pncA 2288778 c.-541_463del frameshift_variant&start_lost 1.0 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
gyrB 5745 p.Ser169* stop_gained 0.12
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
mshA 576147 p.Val267Ala missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761304 p.Val500Phe missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 767010 p.Ser1214* stop_gained 0.13
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 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303823 p.Lys298Arg missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1460962 c.-83G>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475641 n.1984G>T non_coding_transcript_exon_variant 0.12
rrl 1476423 n.2766T>G non_coding_transcript_exon_variant 0.11
inhA 1673736 c.-466G>C upstream_gene_variant 0.13
inhA 1673841 c.-361A>G upstream_gene_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834825 p.His428Gln missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918088 p.Thr50Ile missense_variant 0.17
tlyA 1918490 p.Gln184Arg missense_variant 0.1
ndh 2103226 c.-184C>A upstream_gene_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156083 p.Glu10Gly missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169159 p.Leu485Ser missense_variant 0.12
PPE35 2169866 c.747G>A synonymous_variant 0.14
PPE35 2170558 p.Ala19Thr missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290131 c.-890G>T upstream_gene_variant 0.11
eis 2715541 c.-209A>G upstream_gene_variant 0.11
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475197 c.1194delT frameshift_variant 0.12
whiB7 3568713 c.-34C>G upstream_gene_variant 0.17
Rv3236c 3612276 p.Ser281Pro missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878501 p.Ile3Val missense_variant 0.11
clpC1 4040901 c.-197C>T upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268533 p.Thr102Ser missense_variant 0.1
whiB6 4338371 p.Thr51Pro 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 1.0