TB-Profiler result

Run: SRR6832260
Summary

Run ID: SRR6832260

Sample name:

Date: 04-04-2023 17:19:37

Number of reads: 602884

Percentage reads mapped: 99.57

Strain: lineage2.2.1

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
lineage2.2 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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpoB 761185 p.Glu460Gly missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289171 p.Gly24Asp missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326130 c.1343delA frameshift_variant 1.0 ethionamide, 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 5498 p.Ala87Ser missense_variant 0.11
gyrB 6300 p.Leu354Gln missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8246 c.945C>A synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>T synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575508 p.Thr54Asn missense_variant 0.25
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761796 p.Tyr664His missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763205 c.-165G>A upstream_gene_variant 0.33
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775831 p.Ala884Pro missense_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 778430 c.-560C>T upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800954 p.Ala49Asp missense_variant 0.21
Rv1258c 1406259 p.Pro361Gln missense_variant 0.17
Rv1258c 1406702 c.639C>A synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417197 p.Gly51Arg missense_variant 0.18
atpE 1460860 c.-185C>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.25
rrl 1476671 n.3014A>G non_coding_transcript_exon_variant 0.29
inhA 1673907 c.-295C>A upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834451 p.Leu304Met missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168905 p.Ile570Val missense_variant 0.12
PPE35 2170748 c.-137delA upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746140 p.Gln487* stop_gained 0.18
Rv2752c 3064634 p.Ala520Pro missense_variant 0.14
Rv2752c 3065118 c.1074C>T synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448542 c.39C>T synonymous_variant 0.13
Rv3083 3448755 c.252C>T synonymous_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039539 p.Tyr389Cys missense_variant 0.67
panD 4044413 c.-132T>A upstream_gene_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
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