TB-Profiler result

Run: ERR2514499
Summary

Run ID: ERR2514499

Sample name:

Date: 31-03-2023 20:22:41

Number of reads: 2301291

Percentage reads mapped: 99.35

Strain: lineage4;lineage3;lineage1.1.2

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.05
lineage4 Euro-American LAM;T;S;X;H None 0.06
lineage1 Indo-Oceanic EAI RD239 0.87
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.85
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.84
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.Asp94Ala missense_variant 0.86 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 0.9
gyrB 6124 c.885C>T synonymous_variant 0.9
gyrB 6573 p.Cys445Ser missense_variant 0.85
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.82
gyrA 9047 c.1746C>T synonymous_variant 0.82
gyrA 9143 c.1842T>C synonymous_variant 0.81
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 0.88
fgd1 490754 c.-29C>G upstream_gene_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 0.93
mshA 576000 p.Asp218Ala missense_variant 0.85
rpoB 760490 c.684C>T synonymous_variant 0.83
rpoC 762434 c.-936T>G upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 763884 p.Ala172Val missense_variant 0.9
rpoC 763886 c.517C>A synonymous_variant 0.9
rpoC 765171 p.Pro601Leu missense_variant 0.89
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 776395 p.Phe696Leu missense_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781874 c.315G>A synonymous_variant 0.85
fbiC 1305243 c.2313T>G synonymous_variant 0.86
embR 1417019 p.Cys110Tyr missense_variant 0.71
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103221 c.-179C>T upstream_gene_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.91
PPE35 2167983 p.Gly877Asp missense_variant 0.86
Rv1979c 2222308 p.Asp286Gly missense_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.87
ahpC 2726051 c.-142G>A upstream_gene_variant 0.81
Rv2752c 3064632 c.1560C>T synonymous_variant 0.84
Rv2752c 3065305 p.Ala296Val missense_variant 0.81
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.88
fprA 3475159 p.Asn385Asp missense_variant 0.78
clpC1 4040517 p.Val63Ala missense_variant 0.86
embC 4240671 p.Thr270Ile missense_variant 0.84
embC 4241042 p.Asn394Asp missense_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.9
embA 4245969 p.Pro913Ser missense_variant 0.87
embB 4246958 p.Glu149Lys missense_variant 0.85
embB 4247646 p.Glu378Ala missense_variant 0.75
ubiA 4269387 p.Glu149Asp missense_variant 0.85
aftB 4269606 c.-770T>C upstream_gene_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.87
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407873 c.330G>T synonymous_variant 0.76