TB-Profiler result

Run: SRR6856126
Summary

Run ID: SRR6856126

Sample name:

Date: 04-04-2023 17:56:53

Number of reads: 430975

Percentage reads mapped: 99.62

Strain: lineage2.2.1

Drug-resistance: RR-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
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 8074 p.Glu258Ala missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491312 c.531delC frameshift_variant 0.13
fgd1 491431 p.Ala217Thr missense_variant 0.25
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 761019 p.Ala405Thr missense_variant 0.11
rpoB 762062 p.Asp752Glu missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764910 c.1543dupA frameshift_variant 0.11
rpoC 766967 p.Pro1200Ser missense_variant 0.12
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 1304414 p.Val495Ala missense_variant 0.11
Rv1258c 1406205 p.Thr379Met missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406821 p.Met174Leu missense_variant 0.29
embR 1416864 c.483delC frameshift_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474819 n.1162T>A non_coding_transcript_exon_variant 0.1
fabG1 1673415 c.-25C>A upstream_gene_variant 0.11
rpsA 1833365 c.-177G>T upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
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 2168796 p.Thr606Arg missense_variant 0.11
PPE35 2169995 c.618C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289379 c.-138T>C upstream_gene_variant 0.11
pncA 2289558 c.-318delT upstream_gene_variant 0.13
kasA 2518851 p.Met246Thr missense_variant 0.1
kasA 2519015 p.Ser301Ala missense_variant 0.11
eis 2714325 c.1008C>T synonymous_variant 0.15
eis 2714813 p.Glu174* stop_gained 0.13
folC 2747406 p.Pro65Thr missense_variant 0.15
thyX 3067329 p.Val206Ala missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086854 p.Asn12Ser missense_variant 0.15
ald 3087852 p.Thr345Ser missense_variant 0.22
fprA 3473988 c.-19A>G upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474233 p.Phe76Ser missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641782 p.Val83Ala missense_variant 0.22
fbiB 3642518 c.984C>T synonymous_variant 0.13
clpC1 4038458 c.2247G>T synonymous_variant 0.11
clpC1 4038974 c.1731T>C synonymous_variant 0.11
clpC1 4040894 c.-258_-191delCAGGCGAAAGCCTGGGCGCCGGTACTTTGCCGCGTTCGCTGGCGGCGAACCGATGGCCGCTCGGCGCC upstream_gene_variant 0.24
embC 4240805 p.Arg315Cys missense_variant 0.15
embC 4241978 p.Ser706Pro missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244581 p.Asp450Gly missense_variant 0.22
embA 4244833 p.Val534Ala missense_variant 0.15
embB 4245668 c.-846C>T upstream_gene_variant 0.14
embB 4249020 p.Gly836Glu missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268297 c.540A>G synonymous_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0