TB-Profiler result

Run: SRR6650392
Summary

Run ID: SRR6650392

Sample name:

Date: 15-08-2023 08:01:47

Number of reads: 1146769

Percentage reads mapped: 99.58

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 0.99
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
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 490751 c.-32T>G upstream_gene_variant 0.19
fgd1 490756 c.-27T>G upstream_gene_variant 0.18
fgd1 490759 c.-24A>T upstream_gene_variant 0.18
fgd1 490763 c.-20C>G upstream_gene_variant 0.17
fgd1 490771 c.-12T>G upstream_gene_variant 0.17
fgd1 490787 p.Ala2Gly missense_variant 0.17
fgd1 490790 p.Glu3Gly missense_variant 0.17
fgd1 491014 p.Thr78Pro missense_variant 0.29
fgd1 491027 p.Asn82Thr missense_variant 0.16
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576489 p.Val381Gly missense_variant 0.18
mshA 576723 p.Val459Gly missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.38
ccsA 620756 p.Asp289Gly missense_variant 0.31
ccsA 620770 p.Trp294Arg missense_variant 0.14
ccsA 620773 p.Ile295Val missense_variant 0.27
ccsA 620778 p.Asn296Lys missense_variant 0.15
ccsA 620801 p.Val304Gly missense_variant 0.17
rpoB 759611 c.-196G>C upstream_gene_variant 0.37
rpoB 759615 c.-192A>C upstream_gene_variant 0.44
rpoB 759620 c.-187A>C upstream_gene_variant 0.37
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763501 p.Asp44Glu missense_variant 1.0
rpoC 763849 c.480G>A synonymous_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.17
fbiC 1303016 p.Val29Gly missense_variant 0.2
fbiC 1304159 p.Val410Gly missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461101 c.57T>G synonymous_variant 0.19
atpE 1461108 p.Ile22Leu missense_variant 0.2
atpE 1461131 c.87T>G synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473959 n.302T>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
tlyA 1918029 c.90C>A synonymous_variant 0.15
tlyA 1918052 p.Pro38Arg missense_variant 0.25
ndh 2102524 c.519C>T synonymous_variant 0.15
ndh 2103235 c.-193C>G upstream_gene_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169373 p.Thr414Ala missense_variant 1.0
PPE35 2170072 p.Gly181Arg missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.2
ahpC 2726265 p.Lys25Gln missense_variant 0.19
ahpC 2726269 p.Val26Gly missense_variant 0.29
ahpC 2726338 p.Val49Gly missense_variant 0.3
ahpC 2726341 p.Val50Gly missense_variant 0.27
ahpC 2726343 p.Phe51Val missense_variant 0.17
ahpC 2726350 p.Trp53Leu missense_variant 0.32
ribD 2987323 p.Val162Gly missense_variant 0.29
ribD 2987337 p.Gly167Arg missense_variant 0.18
thyX 3068051 c.-106A>C upstream_gene_variant 0.2
thyA 3074608 c.-137A>G upstream_gene_variant 0.27
thyA 3074633 c.-162C>G upstream_gene_variant 0.17
thyA 3074641 c.-170C>T upstream_gene_variant 0.33
thyA 3074645 c.-174T>G upstream_gene_variant 0.35
thyA 3074648 c.-177T>G upstream_gene_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449738 p.His412Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.16
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.22
embC 4240006 c.144A>C synonymous_variant 0.18
embC 4242387 p.Asn842Thr missense_variant 0.12
embC 4242414 p.Leu851Arg missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249298 p.Trp929Gly missense_variant 0.2
embB 4249305 p.Asn931Thr missense_variant 0.32
embB 4249323 p.Ala937Glu missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268765 c.72T>G synonymous_variant 0.24
aftB 4268776 p.Ser21Gly missense_variant 0.25
ethR 4327597 p.Thr17Pro missense_variant 0.17
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