TB-Profiler result

Run: SRR6650119
Summary

Run ID: SRR6650119

Sample name:

Date: 15-08-2023 07:33:18

Number of reads: 854900

Percentage reads mapped: 99.26

Strain: lineage1.1.3.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA RD239 0.98
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 5433 p.Val65Gly missense_variant 0.18
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
fgd1 491014 p.Thr78Pro missense_variant 0.33
fgd1 491018 p.Phe79Ser missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575926 c.579A>C synonymous_variant 0.17
ccsA 620537 p.Val216Gly missense_variant 0.2
ccsA 620748 c.858T>G synonymous_variant 0.21
ccsA 620756 p.Asp289Gly missense_variant 0.33
ccsA 620759 p.Arg290Pro missense_variant 0.14
ccsA 620761 p.Lys291Gln missense_variant 0.14
ccsA 620770 p.Trp294Arg missense_variant 0.16
ccsA 620801 p.Val304Gly missense_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763849 c.480G>A synonymous_variant 0.25
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764154 p.Gln262Arg missense_variant 0.15
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776912 c.1569G>T synonymous_variant 0.95
mmpL5 777572 c.909C>T synonymous_variant 1.0
mmpR5 779356 p.Arg123Gly missense_variant 0.15
rpsL 781363 c.-197T>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781552 c.-8G>A upstream_gene_variant 0.18
rplC 801287 p.Val160Gly missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474469 n.812T>G non_coding_transcript_exon_variant 0.33
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.5
tlyA 1917776 c.-164G>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917996 c.57A>C synonymous_variant 0.14
tlyA 1918013 p.Glu25Gly missense_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.3
ndh 2103235 c.-193C>G upstream_gene_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169268 p.Gly449Ser missense_variant 0.15
PPE35 2169320 p.Leu431Phe missense_variant 0.15
PPE35 2170064 c.549G>C synonymous_variant 0.2
PPE35 2170072 p.Gly181Arg missense_variant 0.25
PPE35 2170390 p.Trp75Gly missense_variant 0.2
PPE35 2170399 p.Tyr72Asp missense_variant 0.14
PPE35 2170400 c.213G>C synonymous_variant 0.15
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 0.27
kasA 2518151 p.Ser13Arg missense_variant 0.47
kasA 2518161 p.Val16Gly missense_variant 0.36
kasA 2518187 p.Ile25Val missense_variant 0.19
eis 2715037 p.Ala99Gly missense_variant 0.33
eis 2715312 p.Ser7Arg missense_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726267 c.75G>A synonymous_variant 0.21
ahpC 2726269 p.Val26Gly missense_variant 0.21
ahpC 2726279 c.87G>A synonymous_variant 0.23
ahpC 2726688 p.Asp166Tyr missense_variant 0.22
folC 2746745 p.Val285Gly missense_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074645 c.-174T>G upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448638 p.Trp45Cys missense_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449079 p.Leu192Phe missense_variant 0.29
Rv3083 3449093 p.Ala197Gly missense_variant 0.2
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 3611976 p.Ala381Pro missense_variant 0.2
Rv3236c 3612422 p.Val232Gly missense_variant 0.18
fbiA 3641146 p.Ala202Ser missense_variant 0.17
fbiB 3642744 p.Ala404Ser missense_variant 0.18
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.25
clpC1 4039477 p.Met410Val missense_variant 0.19
clpC1 4039484 c.1221T>G synonymous_variant 0.25
clpC1 4039916 c.789T>G synonymous_variant 0.21
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239989 p.Leu43Val missense_variant 0.27
embC 4240017 p.Val52Gly missense_variant 0.25
embC 4240031 p.Ala57Pro missense_variant 0.25
embC 4240461 p.Val200Ala missense_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.23
embC 4242387 p.Asn842Thr missense_variant 0.29
embA 4242406 c.-827A>C upstream_gene_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242920 p.Ala1020Thr missense_variant 0.18
embA 4243347 p.Thr39Pro missense_variant 0.2
embA 4243350 p.Thr40Pro missense_variant 0.36
embA 4243365 p.Trp45Gly missense_variant 0.15
embA 4243372 p.Gln47Arg missense_variant 0.17
embA 4243520 c.288T>G synonymous_variant 0.17
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248553 c.2040C>T synonymous_variant 0.15
embB 4248663 p.Val717Gly missense_variant 0.23
embB 4248677 p.Met722Leu missense_variant 0.2
aftB 4268776 p.Ser21Gly missense_variant 0.22
aftB 4268783 c.54C>G synonymous_variant 0.25
aftB 4268786 c.51C>T synonymous_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269504 c.-668A>G upstream_gene_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326905 p.Leu190Pro missense_variant 0.17
ethR 4326907 c.-642C>G upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0