TB-Profiler result

Run: SRR6207281
Summary

Run ID: SRR6207281

Sample name:

Date: 02-08-2023 15:08:55

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage2.2

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 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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155342 p.Met257Thr missense_variant 0.12 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 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
gyrB 5747 p.Thr170Ala missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9310 p.Asp670Gly missense_variant 0.1
fgd1 490905 c.123T>C synonymous_variant 0.29
fgd1 491027 p.Asn82Thr missense_variant 0.29
fgd1 491080 p.Arg100Gly missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576076 c.729T>C synonymous_variant 0.15
rpoB 759620 c.-187A>C upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776095 p.Arg796Ser missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778722 p.Gly62Cys missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303102 c.172C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473631 n.-27T>A upstream_gene_variant 0.11
rrl 1473913 n.256G>A non_coding_transcript_exon_variant 0.11
rrl 1474132 n.475G>A non_coding_transcript_exon_variant 0.15
rpsA 1833612 p.Ala24Val missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834521 p.Ala327Val missense_variant 0.12
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 2168113 p.Phe834Val missense_variant 0.17
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747002 c.597T>C synonymous_variant 0.11
ribD 2986842 p.Pro2Ser missense_variant 0.1
Rv2752c 3065031 c.1161G>C synonymous_variant 0.12
thyX 3067645 p.Tyr101His missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641333 p.Gly264Val missense_variant 0.11
alr 3840416 c.1005C>T synonymous_variant 0.15
rpoA 3878630 c.-124_-123insC upstream_gene_variant 1.0
embC 4239679 c.-184T>C upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243069 c.-164C>T upstream_gene_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246542 p.Ser10Asn missense_variant 0.15
aftB 4267373 c.1463delT frameshift_variant 0.1
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 4407927 p.Glu92Asp missense_variant 1.0