TB-Profiler result

Run: ERR8025533
Summary

Run ID: ERR8025533

Sample name:

Date: 18-05-2023 01:04:31

Number of reads: 2840935

Percentage reads mapped: 99.68

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.Gly88Cys (1.00)
Moxifloxacin R gyrA p.Gly88Cys (1.00)
Ofloxacin R gyrA p.Gly88Cys (1.00)
Levofloxacin R gyrA p.Gly88Cys (1.00)
Ciprofloxacin R gyrA p.Gly88Cys (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 0.99
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 7563 p.Gly88Cys 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 6650 p.Arg471Cys missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7938 c.638delA frameshift_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491169 c.388delG frameshift_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 0.96
rpoB 759687 c.-120T>A upstream_gene_variant 0.12
rpoB 759752 c.-55G>A upstream_gene_variant 0.2
rpoB 760925 c.1120delA frameshift_variant 0.12
rpoB 761089 p.Ser428Asn missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776107 c.2374C>T synonymous_variant 0.14
mmpL5 776569 p.Met638Val missense_variant 0.15
mmpL5 779175 c.-695G>T 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
rplC 801070 p.Asp88Asn missense_variant 0.2
rplC 801083 p.Ala92Val missense_variant 0.17
rplC 801217 p.Ala137Thr missense_variant 0.12
fbiC 1305290 p.Ser787Asn missense_variant 0.11
Rv1258c 1407518 c.-178C>T upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473656 n.-2G>T upstream_gene_variant 0.13
rrl 1475404 n.1747A>G non_coding_transcript_exon_variant 0.18
rrl 1475632 n.1975C>T non_coding_transcript_exon_variant 0.25
inhA 1673961 c.-241A>G upstream_gene_variant 0.1
rpsA 1833364 c.-178C>G upstream_gene_variant 0.1
rpsA 1833402 c.-140G>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 2102966 p.Gly26Glu missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155045 p.Lys356Arg missense_variant 0.17
katG 2155097 p.Tyr339His missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2222734 p.Phe144Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518384 c.270G>A synonymous_variant 0.12
kasA 2518644 p.Ala177Val missense_variant 0.2
ahpC 2726378 c.186T>C synonymous_variant 0.1
Rv2752c 3064896 c.1296T>C synonymous_variant 0.16
thyX 3067855 c.90delC frameshift_variant 0.11
thyX 3067958 c.-48_-14delCTGCCACACCGAGTTCGTCTAGTTGCGGCCGGCGC upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568653 p.Gln9His missense_variant 0.12
whiB7 3568669 p.Leu4Pro missense_variant 0.12
whiB7 3568852 c.-173G>T upstream_gene_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640540 c.-3G>T upstream_gene_variant 0.13
fbiB 3641049 c.-486T>C upstream_gene_variant 0.14
clpC1 4039972 p.Lys245Glu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249724 p.Val1071Leu missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269089 p.Ala249Thr missense_variant 1.0
whiB6 4338478 p.Phe15Ser missense_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