TB-Profiler result

Run: SRR6650368
Summary

Run ID: SRR6650368

Sample name:

Date: 15-08-2023 08:00:40

Number of reads: 560874

Percentage reads mapped: 99.33

Strain: lineage1.2.2.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.98
lineage1.2.2.2 Indo-Oceanic NA RD239 0.99
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 1.0
gyrB 5530 c.291C>T synonymous_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9701 c.2400T>G synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576723 p.Val459Gly missense_variant 0.33
ccsA 620586 c.696C>T synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.36
ccsA 620752 p.Arg288Gly missense_variant 0.31
ccsA 620756 p.Asp289Gly missense_variant 0.33
ccsA 620773 p.Ile295Val missense_variant 0.25
rpoB 759620 c.-187A>C upstream_gene_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765889 c.2520C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777155 c.1326G>C synonymous_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.2
mmpR5 779348 p.Val120Gly missense_variant 0.39
mmpR5 779356 p.Arg123Gly missense_variant 0.17
mmpR5 779363 p.Leu125Arg missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302948 c.18T>G synonymous_variant 1.0
fbiC 1304166 c.1236A>G synonymous_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461086 c.42A>G synonymous_variant 0.5
atpE 1461125 c.81T>G synonymous_variant 0.4
atpE 1461131 c.87T>G synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833549 p.Ser3Asn missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918059 c.120C>A synonymous_variant 0.25
ndh 2103225 c.-183A>C upstream_gene_variant 0.56
ndh 2103227 c.-185T>C upstream_gene_variant 0.38
ndh 2103235 c.-193C>G upstream_gene_variant 0.71
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167660 p.Thr985Pro missense_variant 0.25
PPE35 2167859 c.2754T>G synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289511 c.-270T>G upstream_gene_variant 0.29
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.27
kasA 2518151 p.Ser13Arg missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726269 p.Val26Gly missense_variant 0.29
pepQ 2859414 c.1005T>G synonymous_variant 0.24
pepQ 2859454 p.Val322Gly missense_variant 0.29
ribD 2987316 p.Ala160Pro missense_variant 0.22
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
Rv2752c 3066103 p.Asn30Ser missense_variant 0.92
thyA 3074641 c.-170C>T upstream_gene_variant 0.29
thyA 3074645 c.-174T>G upstream_gene_variant 0.29
thyA 3074648 c.-177T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.2
fbiD 3339279 c.162T>G synonymous_variant 0.17
fbiD 3339593 p.His159Pro missense_variant 0.19
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.2
fbiB 3642754 p.Leu407Arg missense_variant 0.22
alr 3841515 c.-95C>A upstream_gene_variant 0.14
alr 3841528 c.-108A>C upstream_gene_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 1.0
clpC1 4038163 p.Arg848Gly missense_variant 0.18
clpC1 4038874 p.Thr611Pro missense_variant 0.18
clpC1 4039484 c.1221T>G synonymous_variant 0.27
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240006 c.144A>C synonymous_variant 0.18
embC 4240039 p.Leu59Phe missense_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 0.88
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241433 p.Met524Arg missense_variant 0.33
embC 4242414 p.Leu851Arg missense_variant 0.31
embC 4242422 p.Trp854Gly missense_variant 0.21
embC 4242425 p.Arg855Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242952 c.-281T>G upstream_gene_variant 0.18
embA 4243398 p.Thr56Pro missense_variant 0.2
embA 4244905 p.Val558Gly missense_variant 0.25
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247623 c.1110G>C synonymous_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249190 p.Thr893Pro missense_variant 0.2
embB 4249305 p.Asn931Thr missense_variant 0.25
embB 4249323 p.Ala937Glu missense_variant 0.29
aftB 4268758 p.Ile27Val missense_variant 0.5
aftB 4268774 p.Ser21Gly missense_variant 0.4
aftB 4268786 c.51C>T synonymous_variant 0.75
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269859 c.-26A>C upstream_gene_variant 0.29
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0