TB-Profiler result

Run: SRR6650390
Summary

Run ID: SRR6650390

Sample name:

Date: 15-08-2023 07:39:40

Number of reads: 983993

Percentage reads mapped: 99.38

Strain: lineage4;lineage1.2.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 0.1
lineage1 Indo-Oceanic EAI RD239 0.88
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.94
lineage1.2.2.1 Indo-Oceanic NA RD239 0.92
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 5075 c.-165C>T upstream_gene_variant 0.81
gyrB 6112 p.Met291Ile missense_variant 0.88
gyrA 6382 c.-920A>G upstream_gene_variant 1.0
gyrA 6889 c.-413G>T upstream_gene_variant 0.17
gyrB 6913 p.Asn558Lys missense_variant 0.15
gyrA 6922 c.-380G>T upstream_gene_variant 0.23
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.8
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.93
fgd1 491014 p.Thr78Pro missense_variant 0.21
fgd1 491027 p.Asn82Thr missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575835 p.Trp163Leu missense_variant 0.13
ccsA 619831 c.-60T>G upstream_gene_variant 0.23
ccsA 620748 c.858T>G synonymous_variant 0.17
ccsA 620756 p.Asp289Gly missense_variant 0.22
ccsA 620761 p.Lys291Gln missense_variant 0.22
ccsA 620770 p.Trp294Arg missense_variant 0.15
rpoB 759611 c.-196G>C upstream_gene_variant 0.18
rpoB 759615 c.-192A>C upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 0.9
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpR5 779346 p.Asp119Glu missense_variant 0.17
mmpR5 779348 p.Val120Gly missense_variant 0.23
mmpR5 779363 p.Leu125Arg missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.19
fbiC 1303016 p.Val29Gly missense_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 0.8
embR 1417253 p.Thr32Ser missense_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474756 n.1099T>G non_coding_transcript_exon_variant 0.18
fabG1 1674076 p.Thr213Pro missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918066 p.Ala43Pro missense_variant 0.23
ndh 2103225 c.-183A>C upstream_gene_variant 0.33
ndh 2103235 c.-193C>G upstream_gene_variant 0.35
katG 2154724 p.Arg463Leu missense_variant 0.8
katG 2154819 c.1293C>G synonymous_variant 0.75
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169102 p.Pro504Arg missense_variant 0.13
PPE35 2170082 c.531T>G synonymous_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 0.82
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.17
kasA 2518151 p.Ser13Arg missense_variant 0.22
kasA 2519353 p.Phe413Leu missense_variant 0.77
eis 2714566 p.Leu256Pro missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 0.95
ahpC 2726263 p.Ser24Phe missense_variant 0.2
ahpC 2726265 p.Lys25Gln missense_variant 0.14
ahpC 2726269 p.Val26Gly missense_variant 0.2
ahpC 2726277 p.Lys29Gln missense_variant 0.17
ahpC 2726286 p.Gly32Arg missense_variant 0.25
ahpC 2726338 p.Val49Gly missense_variant 0.14
ahpC 2726341 p.Val50Gly missense_variant 0.21
ahpC 2726345 c.153C>T synonymous_variant 0.2
ahpC 2726350 p.Trp53Leu missense_variant 0.2
ahpC 2726355 p.Lys55Glu missense_variant 0.21
ahpC 2726361 p.Phe57Ile missense_variant 0.14
ahpC 2726378 c.186T>C synonymous_variant 0.14
ahpC 2726382 p.Glu64Gln missense_variant 0.19
ribD 2986935 p.Asp33Asn missense_variant 0.88
ribD 2987314 p.Leu159Pro missense_variant 0.2
ribD 2987323 p.Val162Gly missense_variant 0.27
ribD 2987331 p.Cys165Gly missense_variant 0.2
ribD 2987356 p.Val173Gly missense_variant 0.22
thyA 3074641 c.-170C>T upstream_gene_variant 0.27
thyA 3074645 c.-174T>G upstream_gene_variant 0.25
thyA 3074648 c.-177T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 0.82
ald 3087138 c.319T>C synonymous_variant 0.13
fbiD 3339273 c.156T>G synonymous_variant 0.21
fbiD 3339379 p.Asp88His missense_variant 0.95
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448757 p.Ile85Thr missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.86
fprA 3475159 p.Asn385Asp missense_variant 0.82
Rv3236c 3612137 p.Gly327Ala missense_variant 0.86
Rv3236c 3612835 c.282T>G synonymous_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 0.83
embC 4241042 p.Asn394Asp missense_variant 0.87
embC 4242220 c.2358A>C synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243378 p.Ser49Thr missense_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 0.88
embB 4247646 p.Glu378Ala missense_variant 0.92
embB 4248693 p.Val727Gly missense_variant 0.15
embB 4248730 p.Asn739Lys missense_variant 0.14
embB 4249293 p.Lys927Arg missense_variant 0.15
embB 4249305 p.Asn931Thr missense_variant 0.25
embB 4249323 p.Ala937Glu missense_variant 0.29
aftB 4268776 p.Ser21Gly missense_variant 0.31
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269504 c.-668A>G upstream_gene_variant 0.24
aftB 4269606 c.-770T>C upstream_gene_variant 0.83
ethA 4326439 p.Asn345Lys missense_variant 0.88
ethA 4326887 p.Asp196Gly missense_variant 0.2
ethR 4326898 c.-651C>G upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.89
gid 4407873 c.330G>T synonymous_variant 0.93