TB-Profiler result

Run: SRR6650361
Summary

Run ID: SRR6650361

Sample name:

Date: 15-08-2023 07:38:42

Number of reads: 1151966

Percentage reads mapped: 99.39

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 6917 p.His560Asn missense_variant 0.19
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 491008 p.Thr76Pro missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576700 p.Glu451Asp missense_variant 0.14
mshA 576711 p.Arg455Pro missense_variant 0.15
mshA 576723 p.Val459Gly missense_variant 0.21
mshA 576738 p.Val464Gly missense_variant 0.2
ccsA 620551 p.Asp221Pro missense_variant 0.15
ccsA 620748 c.858T>G synonymous_variant 0.23
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763864 p.Gln165His missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779348 p.Val120Gly missense_variant 0.18
mmpR5 779363 p.Leu125Arg missense_variant 0.21
mmpR5 779369 p.Asp127Ala missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474463 n.806G>A non_coding_transcript_exon_variant 0.15
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.5
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.38
inhA 1673679 c.-523T>G upstream_gene_variant 0.25
fabG1 1674076 p.Thr213Pro missense_variant 0.24
rpsA 1833454 c.-88G>C upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918019 p.Ile27Thr missense_variant 0.15
tlyA 1918031 p.Lys31Arg missense_variant 0.15
tlyA 1918034 p.Val32Gly missense_variant 0.22
tlyA 1918043 p.Asp35Ala missense_variant 0.14
tlyA 1918052 p.Pro38Arg missense_variant 0.27
tlyA 1918055 p.Ala39Gly missense_variant 0.27
tlyA 1918066 p.Ala43Pro missense_variant 0.24
ndh 2103235 c.-193C>G upstream_gene_variant 0.23
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169293 c.1320T>G synonymous_variant 0.31
PPE35 2169317 c.1296C>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.25
kasA 2518151 p.Ser13Arg missense_variant 0.15
kasA 2518161 p.Val16Gly missense_variant 0.25
kasA 2518605 p.Val164Gly missense_variant 0.33
kasA 2518617 p.Val168Gly missense_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726269 p.Val26Gly missense_variant 0.2
ahpC 2726338 p.Val49Gly missense_variant 0.18
ahpC 2726341 p.Val50Gly missense_variant 0.23
ahpC 2726345 c.153C>T synonymous_variant 0.21
ahpC 2726350 p.Trp53Leu missense_variant 0.23
ahpC 2726358 p.Asp56Lys missense_variant 0.17
ahpC 2726363 c.171C>T synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339688 p.Thr191Pro missense_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612557 p.Val187Gly missense_variant 0.28
Rv3236c 3612835 c.282T>G synonymous_variant 0.25
fbiA 3641177 p.Ala212Gly missense_variant 0.18
fbiB 3642749 c.1215T>G synonymous_variant 0.19
fbiB 3642751 p.Asp406Ala missense_variant 0.18
fbiB 3642772 p.Asp413Ala missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242232 c.2370T>C synonymous_variant 0.2
embC 4242414 p.Leu851Arg missense_variant 0.32
embC 4242422 p.Trp854Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244605 p.Val458Gly missense_variant 0.21
embB 4247616 p.Glu368Gly missense_variant 0.19
embB 4249063 c.2550C>T synonymous_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.16
aftB 4268250 p.Ala196Gly missense_variant 0.2
ubiA 4269382 p.Cys151Tyr missense_variant 1.0
ubiA 4269502 p.Val111Gly missense_variant 0.21
aftB 4269504 c.-668A>G upstream_gene_variant 0.19
ubiA 4269833 c.1A>G start_lost 0.2
ubiA 4269859 c.-26A>C upstream_gene_variant 0.14
ethR 4328086 p.Glu180Gln missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0