TB-Profiler result

Run: ERR10748543
Summary

Run ID: ERR10748543

Sample name:

Date: 31-03-2023 10:58:10

Number of reads: 1425089

Percentage reads mapped: 99.85

Strain: lineage4.8.1;lineage1.2.2.1

Drug-resistance: MDR-TB

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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
lineage4 Euro-American LAM;T;S;X;H None 0.4
lineage1 Indo-Oceanic EAI RD239 0.63
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.41
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.63
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.37
lineage1.2.2.1 Indo-Oceanic NA RD239 0.58
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
rpoB 761139 p.His445Cys missense_variant 0.67 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.55 isoniazid
pncA 2289177 c.64delA frameshift_variant 0.74 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.64 ethambutol
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 0.57
gyrB 6112 p.Met291Ile missense_variant 0.65
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.69
gyrA 8452 p.Ala384Val missense_variant 0.66
gyrA 9143 c.1842T>C synonymous_variant 0.59
gyrA 9304 p.Gly668Asp missense_variant 0.68
fgd1 491060 p.Met93Thr missense_variant 0.47
fgd1 491742 c.960T>C synonymous_variant 0.63
ccsA 620659 p.Arg257Cys missense_variant 0.63
rpoC 763031 c.-339T>C upstream_gene_variant 0.68
rpoC 763884 p.Ala172Val missense_variant 0.66
rpoC 763886 c.517C>A synonymous_variant 0.66
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.59
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 0.51
embR 1417019 p.Cys110Tyr missense_variant 0.59
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.49
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.58
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101848 c.1195C>T synonymous_variant 0.67
katG 2154724 p.Arg463Leu missense_variant 0.52
PPE35 2167926 p.Leu896Ser missense_variant 0.66
PPE35 2168149 p.Pro822Ser missense_variant 0.5
Rv1979c 2222308 p.Asp286Gly missense_variant 0.53
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.56
ahpC 2726051 c.-142G>A upstream_gene_variant 0.65
ribD 2987120 c.282C>T synonymous_variant 0.59
ald 3086788 c.-32T>C upstream_gene_variant 0.57
fbiD 3339040 c.-78T>C upstream_gene_variant 0.34
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.58
fprA 3474597 c.591C>A synonymous_variant 0.62
fprA 3474938 p.Glu311Gly missense_variant 0.62
fprA 3475159 p.Asn385Asp missense_variant 0.55
fbiB 3642874 p.Leu447Arg missense_variant 0.23
clpC1 4040517 p.Val63Ala missense_variant 0.55
embC 4240671 p.Thr270Ile missense_variant 0.58
embC 4240750 c.888C>T synonymous_variant 0.52
embC 4241042 p.Asn394Asp missense_variant 0.55
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.58
embB 4247646 p.Glu378Ala missense_variant 0.56
ubiA 4269387 p.Glu149Asp missense_variant 0.66
aftB 4269606 c.-770T>C upstream_gene_variant 0.56
ethA 4326439 p.Asn345Lys missense_variant 0.7
ethR 4327450 c.-99G>A upstream_gene_variant 0.64
ethA 4327602 c.-129C>T upstream_gene_variant 0.69
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.59
gid 4407588 c.615A>G synonymous_variant 0.59
gid 4407873 c.330G>T synonymous_variant 0.6