TB-Profiler result

Run: SRR6484894
Summary

Run ID: SRR6484894

Sample name:

Date: 04-04-2023 14:51:20

Number of reads: 1437966

Percentage reads mapped: 99.72

Strain: lineage4.8;lineage2

Drug-resistance: HR-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 0.47
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.56
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
rpsL 781687 p.Lys43Arg missense_variant 0.53 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid
pncA 2289222 p.Val7Gly missense_variant 0.33 pyrazinamide
ethA 4326707 p.Trp256* stop_gained 0.2 ethionamide
ethA 4326855 p.Arg207Gly missense_variant 0.27 ethionamide
gid 4407851 c.351delG frameshift_variant 0.12 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 0.42
gyrA 9304 p.Gly668Asp missense_variant 0.6
fgd1 491742 c.960T>C synonymous_variant 0.4
mshA 575907 p.Ala187Val missense_variant 0.44
ccsA 620625 p.Ile245Met missense_variant 0.56
rpoC 763031 c.-339T>C upstream_gene_variant 0.38
rpoC 764916 p.Leu516Pro missense_variant 0.36
rpoC 766645 p.Glu1092Asp missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.57
mmpL5 776182 p.Asp767Asn missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.36
atpE 1461182 p.Gln46His missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.86
fabG1 1673380 c.-60C>G upstream_gene_variant 0.11
fabG1 1673629 p.Asp64Asn missense_variant 0.18
inhA 1674923 p.Thr241Arg missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 0.57
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 0.5
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.57
PPE35 2170053 p.Thr187Ser missense_variant 0.53
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715568 c.-236G>A upstream_gene_variant 0.14
folC 2747073 p.Gly176Ser missense_variant 0.17
thyA 3073715 p.Pro253Ala missense_variant 0.22
ald 3087036 p.Lys73* stop_gained 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.5
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.36
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4247395 c.882C>T synonymous_variant 0.55
aftB 4267647 p.Asp397Gly missense_variant 0.44
aftB 4268130 p.Val236Ala missense_variant 0.29
ubiA 4269430 p.Gln135Leu missense_variant 0.2
whiB6 4338371 p.Thr51Pro missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.57
gid 4407927 p.Glu92Asp missense_variant 0.33