TB-Profiler result

Run: SRR6650404
Summary

Run ID: SRR6650404

Sample name:

Date: 15-08-2023 08:03:27

Number of reads: 1233022

Percentage reads mapped: 99.59

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.95
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.97
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.97
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 6645 p.Ser469Asn 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 0.31
fgd1 491014 p.Thr78Pro missense_variant 0.31
fgd1 491027 p.Asn82Thr missense_variant 0.27
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576715 c.1368C>G synonymous_variant 0.27
mshA 576720 p.Glu458Gly missense_variant 0.22
mshA 576723 p.Val459Gly missense_variant 0.4
mshA 576744 p.Val466Gly missense_variant 0.2
ccsA 619707 c.-184T>G upstream_gene_variant 0.2
ccsA 619831 c.-60T>G upstream_gene_variant 0.19
ccsA 619835 c.-56G>T upstream_gene_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759806 c.-1C>T upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766920 p.Ala1184Gly missense_variant 0.14
mmpL5 775603 p.Thr960Pro missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779336 p.Asp116Ala missense_variant 0.3
mmpR5 779346 p.Asp119Glu missense_variant 0.3
mmpR5 779348 p.Val120Gly missense_variant 0.32
mmpR5 779354 p.Leu122Arg missense_variant 0.19
mmpR5 779356 p.Arg123Gly missense_variant 0.33
mmpR5 779363 p.Leu125Arg missense_variant 0.35
mmpR5 779371 p.Ala128Pro missense_variant 0.42
mmpS5 779615 c.-710C>G upstream_gene_variant 0.87
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.29
rplC 801291 c.483C>T synonymous_variant 0.17
rplC 801316 p.Met170Val missense_variant 0.2
fbiC 1303016 p.Val29Gly missense_variant 0.25
Rv1258c 1406452 p.Thr297Pro missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.15
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.18
rrl 1473932 n.275C>A non_coding_transcript_exon_variant 0.17
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.21
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.5
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.4
fabG1 1674076 p.Thr213Pro missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 0.95
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918005 c.66G>A synonymous_variant 0.14
tlyA 1918013 p.Glu25Gly missense_variant 0.19
tlyA 1918052 p.Pro38Arg missense_variant 0.3
tlyA 1918059 c.120C>A synonymous_variant 0.2
tlyA 1918066 p.Ala43Pro missense_variant 0.31
tlyA 1918072 p.Ala45Pro missense_variant 0.15
ndh 2103222 c.-180A>C upstream_gene_variant 0.17
ndh 2103225 c.-183A>C upstream_gene_variant 0.35
ndh 2103227 c.-185T>C upstream_gene_variant 0.3
ndh 2103235 c.-193C>G upstream_gene_variant 0.39
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167845 p.Ser923Asn missense_variant 0.15
PPE35 2167859 c.2754T>G synonymous_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169854 c.759T>G synonymous_variant 0.21
PPE35 2170045 p.Thr190Pro missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289386 c.-145A>C upstream_gene_variant 0.19
pncA 2289509 c.-268A>G upstream_gene_variant 0.2
pncA 2289511 c.-270T>G upstream_gene_variant 0.21
pncA 2289554 c.-313G>T upstream_gene_variant 0.18
kasA 2518147 c.33C>T synonymous_variant 0.33
kasA 2518151 p.Ser13Arg missense_variant 0.41
kasA 2518605 p.Val164Gly missense_variant 0.32
eis 2715560 c.-228T>G upstream_gene_variant 0.24
ahpC 2726265 p.Lys25Gln missense_variant 0.21
ahpC 2726269 p.Val26Gly missense_variant 0.46
ahpC 2726277 p.Lys29Gln missense_variant 0.15
ahpC 2726286 p.Gly32Arg missense_variant 0.5
ahpC 2726290 p.Asp33Gly missense_variant 0.36
folC 2746745 p.Val285Gly missense_variant 0.27
pepQ 2859377 p.Thr348Ala missense_variant 0.18
pepQ 2859414 c.1005T>G synonymous_variant 0.24
pepQ 2859425 p.Gly332Arg missense_variant 0.19
pepQ 2859438 c.981T>G synonymous_variant 0.25
pepQ 2859454 p.Val322Gly missense_variant 0.23
thyA 3073829 p.Gln215Lys missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339174 p.Leu19Phe missense_variant 0.18
fbiD 3339273 c.156T>G synonymous_variant 0.31
fbiD 3339281 p.Ser55Leu missense_variant 0.18
fbiD 3339310 p.Asp65His missense_variant 0.16
Rv3083 3448484 c.-20T>G upstream_gene_variant 0.18
Rv3083 3448765 p.Thr88Pro missense_variant 0.23
Rv3083 3449107 p.Gly202Arg missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.3
fbiB 3642744 p.Ala404Ser missense_variant 0.5
rpoA 3878238 p.Asp90Glu missense_variant 0.3
ddn 3986919 p.Thr26Pro missense_variant 0.2
clpC1 4038163 p.Arg848Gly missense_variant 0.24
clpC1 4039468 p.Arg413Cys missense_variant 0.22
clpC1 4039471 p.Ile412Val missense_variant 0.29
panD 4044471 c.-190T>G upstream_gene_variant 0.18
embC 4239973 c.111T>G synonymous_variant 0.29
embC 4240006 c.144A>C synonymous_variant 0.15
embC 4242220 c.2358A>C synonymous_variant 0.29
embC 4242223 c.2361C>A synonymous_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.24
embC 4242996 p.Val1045Gly missense_variant 0.25
embA 4243350 p.Thr40Pro missense_variant 0.32
embA 4243372 p.Gln47Arg missense_variant 0.16
embA 4243380 p.Thr50Pro missense_variant 0.16
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247614 c.1101T>G synonymous_variant 0.15
embB 4247616 p.Glu368Gly missense_variant 0.15
embB 4247623 c.1110G>C synonymous_variant 0.21
embB 4247657 p.Pro382Thr missense_variant 0.15
embB 4249330 p.Met939Ile missense_variant 0.18
embB 4249757 p.Thr1082Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.96
aftB 4268799 p.Val13Gly missense_variant 0.25
ubiA 4269853 c.-20C>G upstream_gene_variant 0.19
ubiA 4269864 c.-31C>G upstream_gene_variant 0.21
ethR 4327813 p.Thr89Pro missense_variant 0.17
whiB6 4338376 p.Ala49Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0