TB-Profiler result

Run: ERR8025648

Summary

Run ID: ERR8025648

Sample name:

Date: 18-05-2023 04:24:24

Number of reads: 3261130

Percentage reads mapped: 99.6

Strain: lineage2.2.1

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), rpoC p.Leu527Val (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00), katG c.861delA (0.20)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA c.249delC (0.12), pncA c.249delC (0.12)
Streptomycin
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), inhA p.Ile194Thr (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 0.98
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
rpoC 764948 p.Leu527Val missense_variant 1.0 rifampicin
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
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
katG 2155250 c.861delA frameshift_variant 0.2 isoniazid
pncA 2288992 c.249delC frameshift_variant 0.12 pyrazinamide, pyrazinamide
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
gyrB 5699 p.Glu154* stop_gained 0.12
gyrB 5918 p.Ala227Thr missense_variant 0.17
gyrB 6791 p.Asp518Asn missense_variant 0.12
gyrA 6898 c.-404G>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7625 c.324G>T synonymous_variant 0.12
gyrA 8208 p.Glu303* stop_gained 0.18
gyrA 8562 p.Leu421Met missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9699 c.2401_2402dupGT frameshift_variant 0.15
fgd1 491256 p.Lys158Asn missense_variant 0.29
fgd1 491734 p.Arg318Ser missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575941 c.597_600delTACG frameshift_variant 0.15
mshA 576335 p.Pro330Ser missense_variant 0.11
ccsA 619804 c.-87G>T upstream_gene_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760364 c.558C>T synonymous_variant 0.12
rpoB 760374 p.Asp190Asn missense_variant 0.12
rpoB 761172 p.Gly456Ser missense_variant 0.12
rpoB 762730 p.Gln975Arg missense_variant 0.13
rpoC 762779 c.-591C>T upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 763909 c.540C>T synonymous_variant 0.13
rpoC 765179 p.Gly604Arg missense_variant 0.22
rpoC 766368 p.Ala1000Val missense_variant 0.15
rpoC 767308 c.3939C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
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
rplC 800856 c.48A>G synonymous_variant 0.18
fbiC 1303116 c.186C>A synonymous_variant 0.15
fbiC 1303584 c.654C>T synonymous_variant 0.15
fbiC 1304968 c.2038C>T synonymous_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461260 c.216G>A synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471981 n.136C>T non_coding_transcript_exon_variant 0.13
rrs 1472457 n.612A>T non_coding_transcript_exon_variant 0.12
rrl 1473902 n.245T>C non_coding_transcript_exon_variant 0.18
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.12
rrl 1476118 n.2461G>T non_coding_transcript_exon_variant 0.15
rrl 1476593 n.2939delC non_coding_transcript_exon_variant 0.15
rrl 1476742 n.3085A>T non_coding_transcript_exon_variant 0.15
fabG1 1673179 c.-260_-259delCA upstream_gene_variant 0.12
rpsA 1833900 c.361delG frameshift_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917925 c.-15A>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102966 p.Gly26Glu missense_variant 0.15
ndh 2103052 c.-10G>A upstream_gene_variant 0.18
katG 2154099 c.2013G>A synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169896 c.717C>A synonymous_variant 0.2
PPE35 2170175 c.438G>A synonymous_variant 0.13
PPE35 2170765 c.-153G>T upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288858 c.384C>G synonymous_variant 0.12
folC 2746813 c.786A>G synonymous_variant 0.29
folC 2747680 c.-82C>T upstream_gene_variant 0.17
ribD 2987324 c.486G>T synonymous_variant 0.13
Rv2752c 3065545 c.646delA frameshift_variant 0.17
Rv2752c 3066028 p.Pro55Leu missense_variant 0.17
thyX 3067307 c.639C>T synonymous_variant 0.17
thyA 3073906 p.Ala189Val missense_variant 0.29
thyA 3074307 c.165A>G synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087429 p.Leu204Ile missense_variant 0.12
ald 3087552 p.Lys245Glu missense_variant 0.17
fprA 3473869 c.-138A>G upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3473999 c.-8G>A upstream_gene_variant 0.15
fprA 3474043 p.Pro13Ser missense_variant 0.22
fprA 3474060 c.54C>T synonymous_variant 0.2
Rv3236c 3612006 p.Arg371Cys missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641121 c.-414C>T upstream_gene_variant 0.14
fbiB 3641564 c.30G>A synonymous_variant 0.2
fbiB 3642147 p.Val205Ile missense_variant 0.18
fbiB 3642363 p.Glu277Lys missense_variant 0.25
rpoA 3877707 c.801G>A synonymous_variant 0.25
rpoA 3878245 p.Glu88Gly missense_variant 0.12
rpoA 3878383 p.Leu42Pro missense_variant 0.18
ddn 3986721 c.-123G>A upstream_gene_variant 0.11
clpC1 4038608 p.Asp699Glu missense_variant 0.14
clpC1 4038816 p.Ala630Val missense_variant 0.2
clpC1 4039563 c.1139_1141dupTGG conservative_inframe_insertion 0.13
embC 4240125 p.Cys88Tyr missense_variant 0.17
embC 4242165 p.Pro768Leu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244125 c.894delC frameshift_variant 0.12
embA 4244435 c.1203G>A synonymous_variant 0.17
embB 4246786 p.Met91Ile missense_variant 0.15
embB 4246829 p.Gly106Cys missense_variant 0.13
embB 4247455 c.942C>A synonymous_variant 0.12
embB 4247725 c.1212G>T synonymous_variant 0.17
embB 4249232 p.Pro907Ser missense_variant 0.12
embB 4249757 c.3246delC frameshift_variant 0.17
aftB 4267550 c.1286delA frameshift_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268624 c.213C>T synonymous_variant 0.11
ubiA 4269424 p.Ala137Val missense_variant 0.15
aftB 4269737 c.-901C>T upstream_gene_variant 0.2
whiB6 4338297 c.225G>A synonymous_variant 0.22
whiB6 4338540 c.-19T>C upstream_gene_variant 0.13
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 4407943 c.259delC frameshift_variant 0.4