TB-Profiler result

Run: SRR6650303
Summary

Run ID: SRR6650303

Sample name:

Date: 15-08-2023 07:35:55

Number of reads: 1031469

Percentage reads mapped: 99.58

Strain: lineage2.2.1

Drug-resistance: Other

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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 R pncA p.Leu4Ser (1.00)
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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
pncA 2289231 p.Leu4Ser missense_variant 1.0 pyrazinamide
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 6894 p.Met552Arg missense_variant 0.18
gyrB 6920 p.Val561Phe missense_variant 0.13
gyrB 6929 p.Ala564Pro missense_variant 0.21
gyrB 6932 p.Gln565Lys missense_variant 0.14
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 490759 c.-24A>T upstream_gene_variant 0.22
fgd1 490771 c.-12T>G upstream_gene_variant 0.18
fgd1 490780 c.-3C>A upstream_gene_variant 0.2
fgd1 491008 p.Thr76Pro missense_variant 0.27
fgd1 491014 p.Thr78Pro missense_variant 0.57
fgd1 491027 p.Asn82Thr missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575176 c.-172T>G upstream_gene_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576723 p.Val459Gly missense_variant 0.18
ccsA 620545 p.Leu219Val missense_variant 0.15
ccsA 620551 p.Asp221His missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.3
ccsA 620752 p.Arg288Gly missense_variant 0.32
ccsA 620756 p.Asp289Gly missense_variant 0.38
ccsA 620770 p.Trp294Arg missense_variant 0.14
ccsA 620773 p.Ile295Val missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763501 p.Asp44Glu missense_variant 1.0
rpoC 763849 c.480G>A synonymous_variant 0.17
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 779348 p.Val120Gly missense_variant 0.24
mmpR5 779356 p.Arg123Gly missense_variant 0.17
mmpR5 779363 p.Leu125Arg missense_variant 0.12
mmpR5 779371 p.Ala128Pro missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.19
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.67
fabG1 1673668 p.Glu77Lys missense_variant 0.23
fabG1 1673690 p.Val84Gly missense_variant 0.21
fabG1 1674076 p.Thr213Pro missense_variant 0.38
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918044 p.Asp35Glu missense_variant 0.13
tlyA 1918066 p.Ala43Pro missense_variant 0.24
ndh 2103225 c.-183A>C upstream_gene_variant 0.42
ndh 2103235 c.-193C>G upstream_gene_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169317 c.1296C>T synonymous_variant 0.16
PPE35 2169373 p.Thr414Ala missense_variant 1.0
PPE35 2170056 p.Val186Gly missense_variant 0.19
PPE35 2170066 p.Ala183Pro missense_variant 0.19
PPE35 2170082 c.531T>G synonymous_variant 0.32
Rv1979c 2222695 p.Arg157Pro missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288951 c.291T>G synonymous_variant 0.18
pncA 2289574 c.-333T>G upstream_gene_variant 0.22
kasA 2518147 c.33C>T synonymous_variant 0.43
kasA 2518151 p.Ser13Arg missense_variant 0.27
kasA 2518166 p.Ala18Pro missense_variant 0.14
kasA 2518605 p.Val164Gly missense_variant 0.18
eis 2715103 p.Leu77Pro missense_variant 0.21
ahpC 2726345 c.153C>T synonymous_variant 0.13
ahpC 2726506 p.Thr105Lys missense_variant 0.14
ribD 2987316 p.Ala160Pro missense_variant 0.27
ribD 2987323 p.Val162Gly missense_variant 0.35
thyA 3074641 c.-170C>T upstream_gene_variant 0.17
thyA 3074648 c.-177T>G upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.35
fbiD 3339279 c.162T>G synonymous_variant 0.21
Rv3083 3449079 p.Leu192Phe missense_variant 0.18
Rv3083 3449738 p.His412Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.17
Rv3236c 3612780 p.Leu113Val missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.15
fbiB 3642744 p.Ala404Ser missense_variant 0.19
clpC1 4039484 c.1221T>G synonymous_variant 0.23
clpC1 4039806 p.Gly300Ala missense_variant 0.11
embC 4242220 c.2358A>C synonymous_variant 0.5
embC 4242425 p.Arg855Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242908 p.Phe1016Val missense_variant 0.18
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268758 p.Ile27Val missense_variant 0.2
aftB 4268765 c.72T>G synonymous_variant 0.2
aftB 4268776 p.Ser21Gly missense_variant 0.3
ethA 4326092 p.Tyr461Phe missense_variant 0.13
ethA 4326344 p.Ile377Ser missense_variant 0.14
ethA 4326869 p.Val202Gly missense_variant 0.18
ethR 4326880 c.-669G>C upstream_gene_variant 0.15
ethA 4326905 p.Leu190Pro missense_variant 0.13
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