TB-Profiler result

Run: SRR6856054
Summary

Run ID: SRR6856054

Sample name:

Date: 04-04-2023 17:54:30

Number of reads: 795938

Percentage reads mapped: 99.61

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 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
katG 2155290 c.821delA frameshift_variant 0.13 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
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 575517 p.Leu57Pro missense_variant 0.12
mshA 575553 p.Asn69Ser missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764360 p.Asp331Asn missense_variant 0.11
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 776639 c.1842C>T synonymous_variant 0.11
mmpL5 776887 p.Asn532Asp missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781495 c.-65G>A upstream_gene_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472013 n.168A>G non_coding_transcript_exon_variant 0.11
rrs 1472048 n.203T>C non_coding_transcript_exon_variant 0.18
rrs 1472689 n.844C>A non_coding_transcript_exon_variant 0.17
fabG1 1673474 p.Pro12Gln missense_variant 0.18
inhA 1674337 c.136C>T synonymous_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917764 c.-176C>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103226 c.-184C>G upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167864 p.Ser917Thr missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167971 p.Ile881Thr missense_variant 0.13
PPE35 2168129 c.2484G>A synonymous_variant 0.13
PPE35 2169420 p.Asn398Ser missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290150 c.-909T>C upstream_gene_variant 0.18
kasA 2518230 p.Gly39Asp missense_variant 0.18
folC 2746629 p.Asp324Tyr missense_variant 0.2
pepQ 2859637 p.Arg261Leu missense_variant 0.13
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449133 c.630G>A synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475193 p.Lys396Arg missense_variant 0.11
Rv3236c 3612793 c.324C>T synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641293 p.Pro251Ser missense_variant 0.11
fbiB 3642572 c.1038A>G synonymous_variant 0.11
fbiB 3642627 p.Arg365Ser missense_variant 0.11
alr 3840688 c.732delC frameshift_variant 0.11
alr 3840700 p.Met241Val missense_variant 0.1
rpoA 3877834 c.668_673delGGGAAC disruptive_inframe_deletion 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243611 p.Ala127Ser missense_variant 0.11
embA 4243717 p.Leu162Pro missense_variant 0.13
embB 4248171 p.Ala553Val missense_variant 0.11
aftB 4267441 p.Ile466Val missense_variant 0.12
aftB 4267626 p.Tyr404Cys missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338259 p.Arg88Gln missense_variant 0.18
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