TB-Profiler result

Run: SRR5527176
Summary

Run ID: SRR5527176

Sample name:

Date: 04-04-2023 10:36:32

Number of reads: 636119

Percentage reads mapped: 99.62

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674262 p.Ile21Val missense_variant 1.0 isoniazid
pncA 2288935 p.Tyr103Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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
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 619838 c.-53G>T upstream_gene_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763936 c.567C>A synonymous_variant 0.15
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766882 c.3513C>G synonymous_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
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
Rv1258c 1407157 p.Ala62Thr missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475671 n.2014A>G non_coding_transcript_exon_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102738 c.304delG frameshift_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
ribD 2987562 p.His242Asn missense_variant 0.12
ribD 2987610 p.Thr258Ser missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339609 c.492G>C synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642052 p.Leu173Pro missense_variant 0.18
fbiB 3642508 p.Gly325Asp missense_variant 0.12
rpoA 3878431 p.Leu26Pro missense_variant 0.1
clpC1 4039297 p.Ser470Thr missense_variant 0.12
embC 4240844 p.Tyr328His missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 0.92
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244140 p.Pro303Gln missense_variant 0.12
embA 4244574 c.1343delC frameshift_variant 0.33
embA 4244633 c.1401C>A synonymous_variant 0.33
embA 4245131 c.1899G>A synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269319 p.Leu172Pro 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