TB-Profiler result

Run: SRR6981953

Summary

Run ID: SRR6981953

Sample name:

Date: 04-04-2023 18:23:00

Number of reads: 518326

Percentage reads mapped: 98.78

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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
katG 2155734 p.Met126Ile missense_variant 0.12 isoniazid
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 6798 p.Gly520Asp missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.96
fgd1 491346 c.564C>A synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575451 p.Asn35Ser missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576576 p.Ala410Asp missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762763 p.Thr986Met missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
rpoC 765816 p.Thr816Met missense_variant 0.11
rpoC 767108 p.Gly1247Cys missense_variant 0.14
rpoC 767212 c.3843G>T synonymous_variant 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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473596 n.-62G>T upstream_gene_variant 0.13
rrl 1473939 n.282C>A non_coding_transcript_exon_variant 0.29
rrl 1473999 n.342C>T non_coding_transcript_exon_variant 0.22
rrl 1474134 n.477G>C non_coding_transcript_exon_variant 0.12
rrl 1474523 n.868_869dupAC non_coding_transcript_exon_variant 0.12
fabG1 1673298 c.-142A>C upstream_gene_variant 0.12
fabG1 1673471 p.Pro11His missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918621 p.Ser228Gly missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170348 p.Gln89Lys missense_variant 0.4
Rv1979c 2222916 c.246_248delAAC disruptive_inframe_deletion 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289282 c.-41G>T upstream_gene_variant 0.11
pncA 2289421 c.-180C>A upstream_gene_variant 0.11
kasA 2518175 p.Ala21Ser missense_variant 0.11
pepQ 2859330 c.1089C>A synonymous_variant 0.11
thyX 3067584 p.Gly121Asp missense_variant 0.12
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 0.82
fbiA 3641332 p.Gly264Arg missense_variant 1.0
fbiB 3641541 p.Gly3Cys missense_variant 0.14
embC 4242333 p.Gly824Val missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243213 c.-20G>A upstream_gene_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247991 c.1479delG frameshift_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327942 p.Val132Ile missense_variant 0.15
whiB6 4338367 c.154delC frameshift_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407827 p.Asp126Tyr missense_variant 0.14
gid 4407847 p.Ala119Gly missense_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408131 c.72A>G synonymous_variant 0.11