TB-Profiler result

Run: ERR8025618
Summary

Run ID: ERR8025618

Sample name:

Date: 23-05-2023 05:22:53

Number of reads: 3138050

Percentage reads mapped: 99.57

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.Asp435Val (1.00)
Isoniazid R fabG1 c.-17G>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.517dupG (1.00), pncA c.517dupG (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.-17G>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
lineage2.2 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 761110 p.Asp435Val 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 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, 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 5216 c.-24_-23insC upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7448 c.150delC frameshift_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7777 p.Arg159Leu missense_variant 0.14
gyrA 7867 p.Ile189Asn missense_variant 0.14
gyrA 8223 p.Asp308Asn missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9663 p.Ala788Thr missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575707 c.360G>A synonymous_variant 0.15
ccsA 620252 p.Gly121Glu missense_variant 0.14
rpoB 760721 c.915C>T synonymous_variant 0.12
rpoB 760733 p.Lys309Asn missense_variant 0.12
rpoB 760846 p.Thr347Ile missense_variant 0.2
rpoB 762135 p.Asp777Asn missense_variant 1.0
rpoC 762791 c.-579G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763986 p.Arg206His missense_variant 0.12
rpoC 764299 p.Met310Ile missense_variant 0.13
rpoC 765260 p.Ala631Ser missense_variant 0.12
rpoC 765468 c.2101delG frameshift_variant 0.12
rpoC 765873 p.Pro835Arg missense_variant 0.18
rpoC 767273 p.Gly1302Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776130 p.Leu784Pro missense_variant 0.11
mmpL5 777326 c.1155C>G synonymous_variant 0.13
mmpL5 777355 p.Val376Met missense_variant 0.11
mmpL5 777880 p.Asp201His missense_variant 0.17
mmpR5 779109 p.Leu40Phe missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303976 p.Ala349Val missense_variant 0.13
fbiC 1303991 p.Trp354Leu missense_variant 0.13
fbiC 1304804 p.Val625Ala missense_variant 0.13
Rv1258c 1406192 p.Leu383Phe missense_variant 0.13
atpE 1461117 p.Gly25Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472517 n.674delG non_coding_transcript_exon_variant 0.17
rpsA 1833404 c.-138G>T upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102041 p.Gln334His missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170715 c.-103C>T upstream_gene_variant 0.14
PPE35 2170762 c.-150C>A upstream_gene_variant 0.13
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2222683 p.Trp161Leu missense_variant 0.18
Rv1979c 2222752 p.Thr138Met missense_variant 0.12
Rv1979c 2222899 p.Arg89Gln missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289776 c.-535C>T upstream_gene_variant 0.12
kasA 2518555 c.441C>A synonymous_variant 0.14
ahpC 2726288 c.97_101delGACTA frameshift_variant 0.17
folC 2746164 p.Arg479Trp missense_variant 0.15
folC 2746451 p.Gly383Val missense_variant 0.14
folC 2746464 p.Leu379Ile missense_variant 0.17
folC 2746532 p.Pro356Gln missense_variant 0.15
folC 2747007 p.Ser198Gly missense_variant 0.12
folC 2747134 c.465C>A synonymous_variant 0.22
folC 2747454 c.145C>A synonymous_variant 0.13
ribD 2987320 p.Glu161Val missense_variant 0.22
ribD 2987499 p.Gly221Ser missense_variant 0.12
Rv2752c 3064957 p.Ser412Asn missense_variant 0.18
Rv2752c 3064985 c.1207C>T synonymous_variant 0.17
thyA 3074392 c.79dupC frameshift_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087236 c.417A>T synonymous_variant 0.17
fbiD 3339722 p.Gly202Val missense_variant 0.13
Rv3083 3449619 c.1116C>A synonymous_variant 0.18
Rv3083 3449976 p.Asp491Glu missense_variant 0.17
fprA 3473951 c.-56C>T upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475268 p.Ala421Asp missense_variant 0.11
Rv3236c 3611979 p.Ala380Ser missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613016 p.Pro34Leu missense_variant 0.14
Rv3236c 3613123 c.-7T>A upstream_gene_variant 0.13
fbiA 3641350 p.Ala270Ser missense_variant 0.33
fbiB 3641705 p.Glu57Asp missense_variant 0.13
alr 3840222 p.Arg400Met missense_variant 0.14
alr 3840667 p.Arg252Trp missense_variant 0.12
alr 3840925 p.Gly166Cys missense_variant 0.14
clpC1 4039438 p.Glu423* stop_gained 0.17
clpC1 4039746 p.Ile320Thr missense_variant 0.15
panD 4044415 c.-134G>T upstream_gene_variant 0.17
embC 4239849 c.-14C>A upstream_gene_variant 0.12
embC 4240289 p.Pro143Thr missense_variant 0.15
embC 4240320 p.Gln153Arg missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244628 p.Ile466Val missense_variant 0.11
embA 4244886 c.1654C>T synonymous_variant 0.1
embA 4245500 c.2268G>A synonymous_variant 0.11
embB 4247507 c.996delG frameshift_variant 0.13
embB 4247565 p.Arg351His missense_variant 0.14
embB 4247616 p.Glu368Val missense_variant 0.12
embB 4249030 c.2517C>A synonymous_variant 0.12
aftB 4267160 c.1677C>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268611 p.Pro76Ser missense_variant 0.2
ubiA 4268939 p.Val299Ile missense_variant 0.33
ubiA 4269714 p.Leu40Phe missense_variant 0.18
ethR 4327063 c.-486G>A upstream_gene_variant 0.14
ethA 4328243 c.-771delG upstream_gene_variant 0.12
whiB6 4338298 p.Leu75Pro missense_variant 0.1
whiB6 4338461 p.Met21Leu missense_variant 0.12
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
gid 4408407 c.-205C>T upstream_gene_variant 0.15