TB-Profiler result

Run: SRR6855978
Summary

Run ID: SRR6855978

Sample name:

Date: 04-04-2023 17:52:00

Number of reads: 514256

Percentage reads mapped: 99.62

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 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 2155919 p.Ala65Thr missense_variant 0.14 isoniazid
pncA 2289192 p.Gly17Asp missense_variant 0.13 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
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
ccsA 620460 c.570T>A synonymous_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 762770 c.-600C>A upstream_gene_variant 0.17
rpoC 762962 c.-408C>T upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764383 c.1014C>T synonymous_variant 0.15
rpoC 764750 p.Val461Leu 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
mmpR5 779109 c.126_129delGCTG frameshift_variant 0.15
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 1476131 n.2474C>T non_coding_transcript_exon_variant 0.15
rrl 1476338 n.2685delG non_coding_transcript_exon_variant 0.14
fabG1 1673993 p.Tyr185Ser missense_variant 0.12
rpsA 1833646 c.105T>C synonymous_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102135 c.906_907delGG frameshift_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 0.96
katG 2155430 p.Ile228Val missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169483 p.Ala377Glu missense_variant 0.22
PPE35 2169671 c.942C>A synonymous_variant 0.11
PPE35 2169915 p.Gly233Val missense_variant 0.2
PPE35 2170774 c.-162T>C upstream_gene_variant 0.2
Rv1979c 2223076 p.Ala30Val missense_variant 0.14
Rv1979c 2223242 c.-78A>T upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289614 c.-374delT upstream_gene_variant 0.18
kasA 2518690 c.576C>A synonymous_variant 0.18
kasA 2519142 c.1031delG frameshift_variant 0.13
ahpC 2726120 c.-73C>A upstream_gene_variant 0.12
folC 2746628 p.Asp324Val missense_variant 0.12
folC 2747083 c.516G>A synonymous_variant 0.11
Rv2752c 3064745 p.Thr483Ala missense_variant 0.22
Rv2752c 3066219 c.-28T>G upstream_gene_variant 0.14
thyX 3067599 p.Val116Asp missense_variant 0.18
thyA 3074586 c.-115T>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448687 p.Phe62Leu missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568739 c.-60C>T upstream_gene_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640516 c.-27G>A upstream_gene_variant 0.13
alr 3840584 p.Cys279* stop_gained 0.11
rpoA 3877766 p.Ala248Pro missense_variant 0.11
clpC1 4040711 c.-7G>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243541 c.309C>G synonymous_variant 0.1
embA 4244996 c.1764C>A synonymous_variant 0.17
embA 4245249 p.His673Asp missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267929 c.907delC frameshift_variant 0.18
aftB 4268211 p.Arg209His missense_variant 0.13
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