TB-Profiler result

Run: ERR8025719

Summary

Run ID: ERR8025719

Sample name:

Date: 19-05-2023 18:10:21

Number of reads: 3022658

Percentage reads mapped: 99.58

Strain: lineage2.2.2

Drug-resistance: Pre-XDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Cys14Arg (1.00)
Streptomycin R rrs n.514A>C (1.00), gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA p.Ala381Pro (1.00)
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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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 5229 c.-11G>T upstream_gene_variant 0.15
gyrB 5253 p.Lys5Ile missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9514 p.Glu738Val missense_variant 0.12
fgd1 490706 c.-77G>T upstream_gene_variant 0.13
fgd1 490782 c.-1G>T upstream_gene_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575280 c.-68G>A upstream_gene_variant 0.12
mshA 576036 p.Ala230Val missense_variant 0.22
ccsA 620409 c.519C>A synonymous_variant 0.25
ccsA 620858 p.Val323Glu missense_variant 0.11
rpoB 760489 p.Val228Asp missense_variant 0.18
rpoB 760895 c.1089C>T synonymous_variant 0.14
rpoB 760960 p.Val385Asp missense_variant 0.11
rpoB 762023 c.2217C>T synonymous_variant 0.15
rpoB 762772 c.2968delC frameshift_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763790 p.Glu141Lys missense_variant 0.18
rpoC 763953 p.Arg195His missense_variant 0.13
rpoC 764790 p.Arg474His missense_variant 0.12
rpoC 764806 c.1437G>A synonymous_variant 0.12
rpoC 764817 p.Val483Gly missense_variant 0.94
rpoC 765740 c.2372delA frameshift_variant 0.11
rpoC 765951 p.Ala861Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776673 c.1807delG frameshift_variant 0.12
mmpS5 778477 c.429A>G stop_lost&splice_region_variant 0.12
mmpL5 778911 c.-431A>G upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781578 c.19C>T synonymous_variant 0.14
rpsL 781845 p.Lys96Glu missense_variant 0.11
rplC 800636 c.-173C>T upstream_gene_variant 0.12
rplC 801452 p.Gly215Ala missense_variant 0.1
fbiC 1304138 p.Ala403Val missense_variant 0.12
fbiC 1305005 p.Glu692Gly missense_variant 0.12
fbiC 1305211 p.Pro761Ser missense_variant 0.15
fbiC 1305303 c.2373T>C synonymous_variant 0.15
Rv1258c 1406378 c.963C>A synonymous_variant 0.12
Rv1258c 1406740 p.His201Asn missense_variant 0.11
embR 1416370 c.978C>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472470 n.625C>T non_coding_transcript_exon_variant 0.14
rrl 1476706 n.3049C>G non_coding_transcript_exon_variant 0.1
fabG1 1673757 c.320delA frameshift_variant 0.18
inhA 1674102 c.-100C>A upstream_gene_variant 0.13
fabG1 1674140 p.Gly234Asp missense_variant 0.15
rpsA 1833991 c.450C>G synonymous_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918402 p.Leu155Met missense_variant 0.13
ndh 2102040 p.Gly335Cys missense_variant 0.33
ndh 2103047 c.-5G>T upstream_gene_variant 0.15
katG 2154473 p.Gly547Ser missense_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167743 p.Gly957Asp missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169429 p.Gly395Val missense_variant 0.12
PPE35 2170034 c.579G>T synonymous_variant 0.11
PPE35 2170643 c.-32delA upstream_gene_variant 0.11
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289477 c.-236C>A upstream_gene_variant 0.13
pncA 2289576 c.-336delA upstream_gene_variant 0.12
kasA 2518685 p.Asp191Asn missense_variant 0.12
kasA 2519082 p.Ala323Val missense_variant 0.13
eis 2714250 c.1083T>C synonymous_variant 0.17
ahpC 2725928 c.-265C>T upstream_gene_variant 0.15
folC 2746654 c.945C>T synonymous_variant 0.13
folC 2746683 p.Leu306Ile missense_variant 0.18
folC 2747171 p.Gly143Asp missense_variant 0.14
folC 2747517 p.Leu28Met missense_variant 0.25
pepQ 2859816 c.603G>A synonymous_variant 0.17
Rv2752c 3064580 p.Gly538Ser missense_variant 0.12
Rv2752c 3066032 c.159dupC frameshift_variant 0.14
thyX 3067783 p.Ala55Thr missense_variant 0.15
thyX 3067976 c.-31T>C upstream_gene_variant 0.11
thyA 3073877 p.Phe199Leu missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087620 p.Ile267Met missense_variant 0.11
Rv3083 3449147 p.Ser215* stop_gained 0.18
Rv3083 3449272 p.Ala257Thr missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613106 c.10delT frameshift_variant 0.18
fbiB 3642169 p.Thr212Met missense_variant 0.18
alr 3841061 c.360C>T synonymous_variant 0.25
rpoA 3877605 c.903G>T synonymous_variant 0.12
clpC1 4038892 p.Glu605Lys missense_variant 0.12
clpC1 4039213 p.Lys498* stop_gained 0.14
clpC1 4039564 p.Ala381Thr missense_variant 0.15
clpC1 4039689 p.Glu339Gly missense_variant 0.1
clpC1 4039983 p.Thr241Met missense_variant 0.12
clpC1 4040567 c.138C>A synonymous_variant 0.22
panD 4043895 c.387C>A synonymous_variant 0.11
embC 4240813 p.Phe317Leu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243794 p.Arg188Ser missense_variant 0.13
embA 4245009 p.Ala593Ser missense_variant 0.14
embA 4245479 p.Met749Ile missense_variant 0.25
embA 4245643 p.Ala804Val missense_variant 0.14
embA 4246222 p.Leu997His missense_variant 0.12
embB 4246331 c.-183C>T upstream_gene_variant 0.17
embB 4247534 p.Thr341Ala missense_variant 0.29
embB 4248661 c.2148G>T synonymous_variant 0.18
embB 4249121 p.Asp870Tyr missense_variant 0.29
embB 4249298 p.Trp929Arg missense_variant 0.22
embB 4249315 c.2802C>T synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269089 p.Ala249Thr missense_variant 1.0
aftB 4269528 c.-692G>A upstream_gene_variant 0.11
ubiA 4269775 p.Ala20Val missense_variant 0.18
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethA 4326976 c.495_497delGCA disruptive_inframe_deletion 0.12
ethR 4327592 p.Arg15Gln missense_variant 0.15
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