TB-Profiler result

Run: ERR3335730
Summary

Run ID: ERR3335730

Sample name:

Date: 01-04-2023 01:51:52

Number of reads: 6599440

Percentage reads mapped: 99.23

Strain: lineage1.2.2.2

Drug-resistance: HR-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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 0.92
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.91
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.06
lineage1.2.2.2 Indo-Oceanic NA RD239 0.92
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 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2155168 p.Ser315Thr missense_variant 0.1 isoniazid
gid 4408087 c.115delC frameshift_variant 0.87 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 5075 c.-165C>T upstream_gene_variant 0.89
gyrB 6112 p.Met291Ile missense_variant 0.93
gyrA 7268 c.-34C>T upstream_gene_variant 0.91
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.89
gyrA 9143 c.1842T>C synonymous_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.89
rpoC 763886 c.517C>A synonymous_variant 0.89
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.93
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 0.99
tlyA 1918677 c.738G>A synonymous_variant 0.9
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.93
Rv1979c 2222308 p.Asp286Gly missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.93
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.9
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.91
fprA 3475159 p.Asn385Asp missense_variant 0.95
clpC1 4040297 c.408G>A synonymous_variant 0.91
clpC1 4040517 p.Val63Ala missense_variant 0.93
embC 4240671 p.Thr270Ile missense_variant 0.92
embC 4241042 p.Asn394Asp missense_variant 0.91
embC 4241845 c.1983T>C synonymous_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245507 p.Gly759Arg missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 0.93
embB 4247646 p.Glu378Ala missense_variant 0.94
ubiA 4269387 p.Glu149Asp missense_variant 0.87
aftB 4269606 c.-770T>C upstream_gene_variant 0.89
ethA 4326148 c.1326G>T synonymous_variant 0.89
ethA 4326439 p.Asn345Lys missense_variant 0.9
whiB6 4338203 p.Arg107Cys missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.9
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407873 c.330G>T synonymous_variant 0.91