TB-Profiler result

Run: ERR8025601

Summary

Run ID: ERR8025601

Sample name:

Date: 23-05-2023 04:42:34

Number of reads: 2754770

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.Ala90Val (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (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 7570 p.Ala90Val 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 6367 c.1130dupA frameshift_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7400 p.Met33Ile missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8998 p.Leu566* stop_gained 0.13
gyrA 9092 c.1791C>T synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760868 c.1062C>T synonymous_variant 0.13
rpoB 761528 c.1722C>T synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763780 c.411C>A synonymous_variant 0.12
rpoC 764058 p.Ala230Gly missense_variant 0.2
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765205 c.1837delT frameshift_variant 0.13
rpoC 765571 c.2202C>T synonymous_variant 0.14
rpoC 765993 p.Arg875Gln missense_variant 0.18
rpoC 766788 p.Glu1140Gly missense_variant 0.12
rpoC 766884 p.Ser1172Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777386 c.1095C>T synonymous_variant 0.12
mmpR5 779029 p.Pro14Ser missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303959 c.1029C>T synonymous_variant 0.12
Rv1258c 1407003 p.Ala113Val missense_variant 0.14
Rv1258c 1407186 p.Met52Thr missense_variant 0.1
atpE 1460847 c.-198G>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472964 n.1119C>T non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>A non_coding_transcript_exon_variant 0.15
rrl 1476489 n.2832C>T non_coding_transcript_exon_variant 0.18
fabG1 1673174 c.-266_-265delCGinsTA upstream_gene_variant 0.14
fabG1 1673324 c.-116G>A upstream_gene_variant 0.11
inhA 1674777 c.576C>T synonymous_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154451 p.Lys554Arg missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221863 c.1302C>T synonymous_variant 0.1
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746397 p.Val401Asp missense_variant 0.15
folC 2747523 p.Ser26Thr missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449937 c.1434C>T synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612521 p.Ser199Leu missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877671 c.837C>T synonymous_variant 0.16
embC 4241114 p.Ala418Thr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.12
embB 4246516 c.3G>T start_lost 0.12
embB 4248544 c.2031G>A synonymous_variant 0.12
embB 4249536 p.Glu1008Gly missense_variant 0.1
aftB 4267370 c.1467C>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267721 c.1116C>T synonymous_variant 0.17
aftB 4268093 c.744C>T synonymous_variant 0.12
aftB 4268687 c.150C>T synonymous_variant 0.13
ubiA 4269089 p.Ala249Thr missense_variant 1.0
ethA 4326563 p.Ala304Val 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