TB-Profiler result

Run: SRR6824379

Summary

Run ID: SRR6824379

Sample name:

Date: 12-08-2022 08:24:06

Number of reads: 10711904

Percentage reads mapped: 99.4

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB


Download CSV Download TXT Download PDF Download JSON
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 7570 p.Ala90Val missense_variant 0.57 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761082 c.1279_1284delACCAGC conservative_inframe_deletion 1.0 rifampicin
rpsL 781822 p.Lys88Met missense_variant 0.99 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.56 isoniazid, ethionamide
katG 2155412 p.Gly234Arg missense_variant 1.0 isoniazid
pncA 2289103 p.Thr47Ala missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
ethA 4326705 c.768dupG frameshift_variant 0.3 ethionamide
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 6737 p.Thr500Asp missense_variant 0.27
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 491051 p.Phe90Ser missense_variant 0.14
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
rpoB 760321 p.Gln172Arg missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764832 p.Glu488Gly missense_variant 0.99
rpoC 765513 p.Lys715Thr missense_variant 0.55
rpoC 766809 p.Val1147Ala missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.99
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
rrs 1471893 n.48T>C non_coding_transcript_exon_variant 0.5
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065453 p.Gln247* stop_gained 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 4038746 c.1959C>G synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248581 p.Pro690Ser missense_variant 0.99
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326554 p.His307Pro missense_variant 0.16
whiB6 4338365 p.Cys53Gly missense_variant 0.35
whiB6 4338473 c.49A>C synonymous_variant 0.11
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