TB-Profiler result

Run: SRR6650426
Summary

Run ID: SRR6650426

Sample name:

Date: 04-04-2023 15:24:44

Number of reads: 818618

Percentage reads mapped: 99.58

Strain: lineage2.2.1.1

Drug-resistance: Other

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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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.99
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 7570 p.Ala90Val missense_variant 0.33 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Tyr missense_variant 0.6 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.14 streptomycin
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 575460 p.Val38Ala missense_variant 0.15
mshA 575475 p.Asp43Val missense_variant 0.15
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
mmpL5 775639 p.Ile948Val missense_variant 0.92
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776174 c.2307C>A synonymous_variant 0.15
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778754 p.Phe51Tyr missense_variant 0.12
mmpR5 779395 p.Leu136Met missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303573 c.643C>T synonymous_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472453 n.608G>T non_coding_transcript_exon_variant 0.1
fabG1 1673357 c.-83G>A upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
inhA 1674185 c.-17A>G upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103131 c.-89C>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.67
Rv1979c 2221895 p.Val424Ile missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
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 1.0
clpC1 4038276 p.Glu810Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248308 p.Phe599Ile missense_variant 0.2
embB 4249690 c.3177C>T synonymous_variant 0.15
aftB 4266958 p.Glu627Lys missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407732 c.471G>A synonymous_variant 0.94
gid 4407927 p.Glu92Asp missense_variant 1.0