TB-Profiler result

Run: SRR6650114
Summary

Run ID: SRR6650114

Sample name:

Date: 15-08-2023 07:33:19

Number of reads: 978362

Percentage reads mapped: 99.3

Strain: lineage1.2.2.2

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 0.91
gyrA 7268 c.-34C>T upstream_gene_variant 0.94
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 8525 c.1224C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491014 p.Thr78Pro missense_variant 0.26
fgd1 491414 p.Val211Gly missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576698 p.Glu451Gln missense_variant 0.17
mshA 576723 p.Val459Gly missense_variant 0.18
mshA 576732 p.Asp462Gly missense_variant 0.22
ccsA 619831 c.-60T>G upstream_gene_variant 0.18
ccsA 620752 p.Arg288Gly missense_variant 0.23
ccsA 620756 p.Asp289Gly missense_variant 0.27
ccsA 620763 c.873G>A synonymous_variant 0.19
ccsA 620773 p.Ile295Val missense_variant 0.21
rpoB 760000 p.Arg65Pro missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.93
rpoC 763886 c.517C>A synonymous_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.22
mmpR5 779346 p.Asp119Glu missense_variant 0.18
mmpR5 779348 p.Val120Gly missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781649 c.90T>G synonymous_variant 0.14
rplC 801287 p.Val160Gly missense_variant 0.31
fbiC 1303016 p.Val29Gly missense_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460860 c.-185C>T upstream_gene_variant 0.94
atpE 1461086 c.42A>G synonymous_variant 0.33
atpE 1461101 c.57T>G synonymous_variant 0.18
atpE 1461108 p.Ile22Leu missense_variant 0.17
atpE 1461119 c.75T>G synonymous_variant 0.25
atpE 1461125 c.81T>G synonymous_variant 0.29
atpE 1461131 c.87T>G synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.67
fabG1 1673690 p.Val84Gly missense_variant 0.25
fabG1 1674076 p.Thr213Pro missense_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917993 c.54A>G synonymous_variant 0.4
ndh 2103235 c.-193C>G upstream_gene_variant 0.23
katG 2153914 p.Asn733Thr missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156440 c.-329A>T upstream_gene_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 0.9
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169845 p.Asn256Lys missense_variant 0.18
PPE35 2169854 c.759T>G synonymous_variant 0.23
PPE35 2170390 p.Trp75Gly missense_variant 0.2
Rv1979c 2222189 p.Leu326Ile missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
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 0.33
kasA 2518151 p.Ser13Arg missense_variant 0.23
kasA 2518155 p.Val14Gly missense_variant 0.21
kasA 2518161 p.Val16Gly missense_variant 0.21
kasA 2518219 c.105T>G synonymous_variant 0.19
eis 2715117 c.216T>G synonymous_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.29
ahpC 2726269 p.Val26Gly missense_variant 0.25
ahpC 2726363 c.171C>T synonymous_variant 0.2
ahpC 2726640 p.Thr150Pro missense_variant 0.21
folC 2746696 p.Asn301Lys missense_variant 0.17
pepQ 2859367 p.Met351Lys missense_variant 0.2
pepQ 2859375 c.1044G>C synonymous_variant 0.14
Rv2752c 3065591 p.Cys201Gly missense_variant 0.18
thyA 3074641 c.-170C>T upstream_gene_variant 0.18
thyA 3074645 c.-174T>G upstream_gene_variant 0.24
ald 3086627 c.-193A>G upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339688 p.Thr191Pro missense_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448762 p.Asp87Asn missense_variant 0.18
Rv3083 3448765 p.Thr88Pro missense_variant 0.33
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 3611983 c.1134G>C synonymous_variant 0.2
fbiB 3642707 c.1173C>G synonymous_variant 0.19
fbiB 3642772 p.Asp413Ala missense_variant 0.31
clpC1 4039433 c.1272C>T synonymous_variant 0.14
clpC1 4040234 c.471C>A synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.19
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240684 p.Asp274Glu missense_variant 0.18
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.33
embC 4242230 p.Ile790Phe missense_variant 0.22
embC 4242371 p.Ala837Pro missense_variant 0.18
embC 4242422 p.Trp854Gly missense_variant 0.22
embC 4242425 p.Arg855Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242952 c.-281T>G upstream_gene_variant 0.18
embC 4243062 p.Tyr1067Ser missense_variant 0.17
embA 4243347 p.Thr39Pro missense_variant 0.24
embA 4243350 p.Thr40Pro missense_variant 0.22
embA 4243367 p.Trp45Cys missense_variant 0.19
embA 4244617 p.Ala462Gly missense_variant 0.18
embA 4245353 c.2121G>A synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247616 p.Glu368Gly missense_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268776 p.Ser21Gly missense_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4326905 p.Leu190Pro missense_variant 0.23
ethR 4327813 p.Thr89Pro missense_variant 0.2
ethR 4327816 p.Leu90Ile missense_variant 0.13
whiB6 4338203 p.Arg107Cys missense_variant 1.0
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 1.0
gid 4407873 c.330G>T synonymous_variant 1.0