TB-Profiler result

Run: SRR671770
Summary

Run ID: SRR671770

Sample name:

Date: 04-04-2023 15:27:21

Number of reads: 5522272

Percentage reads mapped: 99.49

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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2154979 p.Leu378Pro missense_variant 1.0 isoniazid
pncA 2289103 p.Thr47Ala missense_variant 0.99 pyrazinamide
embB 4247730 p.Gly406Ala 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 491564 p.Ser261Asn missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762564 p.Met920Val missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.26
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 764821 p.Trp484Cys missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715120 c.213G>T synonymous_variant 1.0
ahpC 2726121 c.-72C>T upstream_gene_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.41
Rv2752c 3064552 p.Arg547Pro missense_variant 0.25
Rv2752c 3065129 c.1063C>T synonymous_variant 1.0
thyX 3067426 p.Val174Met missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448456 c.-48G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612037 p.Phe360Leu missense_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.12
embC 4239842 c.-21C>A upstream_gene_variant 0.11
embC 4242425 p.Arg855Gly missense_variant 0.22
embC 4242476 p.Pro872Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.45
embA 4243460 c.228C>T synonymous_variant 0.99
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269125 p.Ala237Thr missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.24
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338594 c.-73T>G upstream_gene_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 0.99