TB-Profiler result

Run: SRR11972371
Summary

Run ID: SRR11972371

Sample name:

Date: 03-04-2023 05:39:04

Number of reads: 652458

Percentage reads mapped: 97.86

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
gyrA 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 5590 c.351T>C synonymous_variant 0.17
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 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.28
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoB 759618 c.-189T>C upstream_gene_variant 0.22
rpoB 761388 p.Asp528Asn missense_variant 0.13
rpoB 761827 p.His674Arg missense_variant 1.0
rpoB 762447 p.Gly881Ser missense_variant 0.2
rpoB 762454 p.His883Arg missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 779275 p.Arg96Trp 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 1304903 p.Glu658Val missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416526 c.822C>G synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289193 p.Gly17Cys missense_variant 1.0
Rv2752c 3064582 p.Val537Ala missense_variant 0.11
Rv2752c 3067039 c.-848T>C upstream_gene_variant 1.0
thyA 3073733 p.Val247Ile missense_variant 0.11
thyA 3073820 p.Leu218Met missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.13
fprA 3473970 c.-37C>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.16
clpC1 4039526 c.1179G>C synonymous_variant 0.14
clpC1 4039530 p.Asp392Ala missense_variant 0.13
embC 4240367 p.Val169Ile missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240843 c.981C>T synonymous_variant 0.12
embC 4240847 p.Asp329Asn missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245794 c.-720G>T upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326925 p.Ser183Arg 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