TB-Profiler result

Run: SRR6650365
Summary

Run ID: SRR6650365

Sample name:

Date: 15-08-2023 08:01:56

Number of reads: 1512801

Percentage reads mapped: 99.52

Strain: lineage2.2.1

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
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 5353 c.114T>G synonymous_variant 0.24
gyrB 5362 c.123T>G synonymous_variant 0.24
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 490696 c.-87T>G upstream_gene_variant 0.25
fgd1 490751 c.-32T>G upstream_gene_variant 0.18
fgd1 491014 p.Thr78Pro missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575704 c.357T>G synonymous_variant 0.21
mshA 575907 p.Ala187Val missense_variant 0.9
mshA 575926 c.579A>C synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.38
rpoB 761890 p.Val695Gly missense_variant 0.23
rpoB 762958 p.Leu1051Arg missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765237 p.Asp623Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779363 p.Leu125Gln missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.3
fbiC 1303038 c.108T>G synonymous_variant 0.23
fbiC 1303174 p.Leu82Val missense_variant 0.22
fbiC 1304159 p.Val410Gly missense_variant 0.22
fbiC 1304161 p.Arg411Gly missense_variant 0.22
fbiC 1304194 p.Thr422Pro missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473945 n.288T>G non_coding_transcript_exon_variant 0.3
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.33
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.27
rrl 1473973 n.316T>G non_coding_transcript_exon_variant 0.27
rrl 1475029 n.1372T>G non_coding_transcript_exon_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
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 2169285 p.Tyr443Phe missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170223 c.390T>C synonymous_variant 0.22
PPE35 2170383 p.Ala77Gly missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517933 c.-182T>G upstream_gene_variant 0.2
kasA 2519186 p.Thr358Pro missense_variant 0.22
ahpC 2726338 p.Val49Gly missense_variant 0.53
ahpC 2726341 p.Val50Gly missense_variant 0.4
ahpC 2726343 p.Phe51Val missense_variant 0.27
ahpC 2726350 p.Trp53Leu missense_variant 0.14
ahpC 2726367 p.Phe59Val missense_variant 0.21
folC 2746161 p.Thr480Ala missense_variant 0.27
folC 2746174 c.1425A>C synonymous_variant 0.17
folC 2747229 p.Tyr124His missense_variant 0.14
folC 2747778 c.-180T>C upstream_gene_variant 0.21
pepQ 2859778 p.Val214Gly missense_variant 0.17
ribD 2987042 c.204A>C synonymous_variant 0.17
ribD 2987439 p.Thr201Ala missense_variant 0.24
Rv2752c 3064766 p.Thr476Pro missense_variant 0.24
Rv2752c 3066221 c.-30T>G upstream_gene_variant 0.13
thyX 3067995 c.-50A>C upstream_gene_variant 0.21
thyX 3068024 c.-79A>C upstream_gene_variant 0.32
thyX 3068031 c.-86A>C upstream_gene_variant 0.22
thyX 3068042 c.-97T>C upstream_gene_variant 0.29
thyX 3068051 c.-106A>C upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087909 p.Thr364Pro missense_variant 0.2
fbiD 3339279 c.162T>G synonymous_variant 0.31
fbiD 3339553 p.Thr146Ala missense_variant 0.27
fbiD 3339749 p.Val211Gly missense_variant 0.25
fbiD 3339755 p.His213Pro missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475286 p.Asp427Ala missense_variant 0.19
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612965 p.Val51Gly missense_variant 0.22
fbiA 3640372 c.-171A>G upstream_gene_variant 1.0
fbiA 3640387 c.-156G>A upstream_gene_variant 1.0
fbiB 3641815 p.Ile94Thr missense_variant 0.23
fbiB 3642751 p.Asp406Ala missense_variant 0.2
fbiB 3642779 c.1245A>C synonymous_variant 0.18
clpC1 4039484 c.1221T>G synonymous_variant 0.5
panD 4043963 p.Phe107Val missense_variant 0.2
embC 4241456 p.Ala532Pro missense_variant 0.2
embC 4242549 p.Val896Gly missense_variant 0.22
embA 4242598 c.-635T>G upstream_gene_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 0.93
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244276 c.1044A>C synonymous_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4247033 p.Ser174Arg missense_variant 0.18
embB 4249316 p.Ala935Pro missense_variant 0.27
embB 4249403 p.Thr964Pro missense_variant 0.18
embB 4249757 p.Thr1082Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268776 p.Ser21Gly missense_variant 0.23
ubiA 4269828 p.Ser2Arg missense_variant 0.29
ethA 4328468 c.-995T>G upstream_gene_variant 0.15
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