TB-Profiler result

Run: ERR4822004

Summary

Run ID: ERR4822004

Sample name:

Date: 20-10-2023 09:47:30

Number of reads: 2401747

Percentage reads mapped: 91.28

Strain: lineage1.1.1.1

Drug-resistance: Other


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
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rrs n.888G>A (0.47)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.99
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.47 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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8045 c.744C>T synonymous_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777581 p.Tyr300* stop_gained 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.8
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.36
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.36
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.64
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.54
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.62
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.45
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.35
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.73
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.79
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.92
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.86
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.85
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.83
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.92
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.83
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.82
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.38
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.43
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.49
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.47
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.38
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.83
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.7
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.64
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.75
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.44
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.45
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.78
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.78
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.83
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.86
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.52
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.52
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.86
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.85
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.89
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.88
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.76
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.56
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.74
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.29
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.39
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.62
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.47
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.76
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.7
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.46
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.7
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.93
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.57
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.54
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.92
inhA 1674622 p.Gly141Arg missense_variant 1.0
rpsA 1834319 p.Val260Ile missense_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156389 c.-278G>C upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168981 c.1632A>G synonymous_variant 1.0
PPE35 2168985 p.Thr543Met missense_variant 1.0
PPE35 2168987 p.Thr542Ala missense_variant 1.0
PPE35 2168990 c.1623T>G synonymous_variant 1.0
PPE35 2169041 c.1572G>A synonymous_variant 1.0
PPE35 2169053 c.1560T>C synonymous_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.98
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4328440 c.-967G>C upstream_gene_variant 1.0
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0