TB-Profiler result

Run: SRR23310812
Summary

Run ID: SRR23310812

Sample name:

Date: 13-03-2023 22:58:49

Number of reads: 176644

Percentage reads mapped: 99.67

Strain: lineage2

Drug-resistance: MDR-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
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4327033 p.Tyr147* stop_gained 1.0 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 5117 c.-123G>A upstream_gene_variant 0.22
gyrA 6631 c.-671C>T upstream_gene_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9513 p.Glu738Lys missense_variant 0.33
fgd1 491617 p.Gln279* stop_gained 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620539 p.Arg217Trp missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620660 p.Arg257His missense_variant 1.0
rpoB 760784 c.978G>A synonymous_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763870 c.501C>T synonymous_variant 0.5
rpoC 764840 p.Ile491Val missense_variant 1.0
rpoC 766041 c.2674delC frameshift_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775849 p.Gly878Arg missense_variant 0.4
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776741 c.1740C>T synonymous_variant 0.4
mmpL5 777584 c.897C>T synonymous_variant 0.17
mmpL5 777649 p.Ala278Thr missense_variant 0.15
mmpS5 779588 c.-683C>A upstream_gene_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305368 p.Glu813Gly missense_variant 0.67
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407484 c.-144C>A upstream_gene_variant 0.29
embR 1416229 c.1119C>T synonymous_variant 0.4
embR 1417255 c.90delG frameshift_variant 0.4
embR 1417297 c.49delG frameshift_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472007 n.162G>T non_coding_transcript_exon_variant 0.33
rrl 1474930 n.1273A>T non_coding_transcript_exon_variant 0.17
rrl 1476024 n.2367T>C non_coding_transcript_exon_variant 0.33
fabG1 1673351 c.-89G>A upstream_gene_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102210 p.Ala278Val missense_variant 0.67
katG 2155118 p.Phe332Leu missense_variant 0.33
PPE35 2167741 p.Thr958Ala missense_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222014 p.Val384Ala missense_variant 0.18
Rv1979c 2222962 p.Ala68Val missense_variant 0.29
folC 2746255 c.1344C>T synonymous_variant 0.4
folC 2746918 c.681G>A synonymous_variant 0.4
pepQ 2859329 p.Arg364Trp missense_variant 0.25
pepQ 2859466 p.Ala318Val missense_variant 0.67
Rv2752c 3065845 p.Cys116Tyr missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473837 c.-170A>G upstream_gene_variant 0.25
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613199 c.-83G>A upstream_gene_variant 0.29
alr 3841476 c.-56G>A upstream_gene_variant 0.5
rpoA 3877750 p.Asp253Gly missense_variant 1.0
clpC1 4038187 p.Ala840Thr missense_variant 0.29
clpC1 4040198 c.507G>A synonymous_variant 0.29
clpC1 4040536 p.Glu57* stop_gained 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>A upstream_gene_variant 1.0
embA 4244213 c.981C>T synonymous_variant 0.2
embB 4246806 p.Val98Glu missense_variant 0.25
embB 4247333 p.Arg274Cys missense_variant 0.4
embB 4248319 c.1806A>T synonymous_variant 0.29
aftB 4267334 p.Asp501Glu missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269947 c.-114G>A upstream_gene_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338684 c.-163C>G upstream_gene_variant 0.5
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0