TB-Profiler result

Run: ERR8025477
Summary

Run ID: ERR8025477

Sample name:

Date: 17-05-2023 23:00:18

Number of reads: 3402756

Percentage reads mapped: 99.61

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

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 R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Tyr103* (1.00)
Streptomycin R rpsL p.Lys43Arg (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
Amikacin
Capreomycin
Kanamycin R eis c.-10G>C (1.00), eis c.-10G>C (1.00)
Cycloserine R ald c.464delG (0.78)
Ethionamide R fabG1 c.-15C>T (1.00), ethR p.Ala95Thr (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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288933 p.Tyr103* stop_gained 1.0 pyrazinamide
eis 2715342 c.-10G>C upstream_gene_variant 1.0 kanamycin, kanamycin
ald 3087278 c.464delG frameshift_variant 0.78 cycloserine
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 1.0 ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7705 p.Thr135Ile missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576387 p.Ala347Val missense_variant 0.2
ccsA 619728 c.-163C>T upstream_gene_variant 0.25
ccsA 620451 c.561G>T synonymous_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761302 p.Arg499Gln missense_variant 0.14
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 762932 c.-438G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 764566 c.1197C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776114 c.2367C>A synonymous_variant 0.18
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778063 p.Gln140* stop_gained 0.14
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303859 p.Gly310Val missense_variant 0.17
fbiC 1304327 p.Leu466Pro missense_variant 0.11
fbiC 1304367 p.Gln479His missense_variant 0.13
fbiC 1304920 p.Ile664Val missense_variant 0.13
fbiC 1304973 c.2043C>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417241 p.Arg36Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473429 n.-229G>A upstream_gene_variant 0.15
rrl 1474164 n.507C>A non_coding_transcript_exon_variant 0.33
rrl 1474507 n.850G>A non_coding_transcript_exon_variant 0.18
rrl 1475208 n.1551C>A non_coding_transcript_exon_variant 0.17
rrl 1475503 n.1846C>A non_coding_transcript_exon_variant 0.15
rrl 1476575 n.2918C>T non_coding_transcript_exon_variant 0.22
inhA 1674430 p.Arg77Trp missense_variant 0.12
inhA 1674735 p.Glu178Asp missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834901 p.Ala454Thr missense_variant 0.17
rpsA 1834908 p.Ser456Leu missense_variant 0.17
rpsA 1834931 c.1390C>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102322 p.Val241Met missense_variant 0.86
ndh 2102346 p.Ala233Thr missense_variant 0.16
ndh 2102909 p.Arg45His missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154897 c.1215C>T synonymous_variant 0.13
katG 2154984 c.1128G>T synonymous_variant 0.12
katG 2156026 p.Pro29Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170186 p.Met143Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289960 c.-719C>A upstream_gene_variant 0.13
kasA 2518397 c.286delG frameshift_variant 0.25
kasA 2519093 p.Arg327Cys missense_variant 0.17
ahpC 2726654 c.462G>T synonymous_variant 0.14
folC 2746771 c.828A>G synonymous_variant 0.14
folC 2747324 p.Arg92His missense_variant 0.15
pepQ 2859603 c.816G>T synonymous_variant 0.12
pepQ 2860189 p.Arg77Leu missense_variant 0.17
thyA 3073690 p.Val261Gly missense_variant 0.12
thyA 3073933 p.Ser180Thr missense_variant 0.16
thyA 3074464 p.Pro3Leu missense_variant 0.66
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087670 c.853dupC frameshift_variant 0.18
fbiD 3339309 c.192C>A synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474035 p.Gly10Ala missense_variant 0.17
fprA 3474414 c.408A>G synonymous_variant 0.22
fprA 3474441 c.435G>A synonymous_variant 0.17
fprA 3475002 c.996G>A synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641448 c.-87G>T upstream_gene_variant 0.13
fbiB 3642110 c.576C>T synonymous_variant 0.12
clpC1 4038762 p.Thr648Ile missense_variant 0.13
clpC1 4040010 p.Ala232Asp missense_variant 0.15
clpC1 4040013 p.Gln231Arg missense_variant 0.15
embC 4240422 p.Glu187Gly missense_variant 0.1
embC 4242319 p.Glu819Asp missense_variant 0.15
embA 4242337 c.-896C>T upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243152 c.-81G>T upstream_gene_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244389 p.Ala386Val missense_variant 0.13
embB 4247108 p.Gly199Trp missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267674 p.Trp388Leu missense_variant 0.13
ethA 4327746 c.-273T>A upstream_gene_variant 0.11
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