TB-Profiler result

Run: ERR4796779

Summary

Run ID: ERR4796779

Sample name:

Date: 01-04-2023 07:06:08

Number of reads: 4326715

Percentage reads mapped: 99.55

Strain: lineage3.1.2

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.96
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.97
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.96
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.Asp94Gly missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.95 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 0.96 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.96 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.93 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9758 c.2457C>T synonymous_variant 0.96
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576113 p.Arg256Gly missense_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 0.97
rpoC 762434 c.-936T>G upstream_gene_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 767123 p.Val1252Leu missense_variant 0.96
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
tlyA 1918104 c.165G>A synonymous_variant 0.93
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.96
PPE35 2170065 p.Ala183Gly missense_variant 0.3
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.97
pncA 2289365 c.-125delC upstream_gene_variant 0.96
ahpC 2726105 c.-88G>A upstream_gene_variant 0.93
pepQ 2860159 p.Ala87Gly missense_variant 0.17
thyA 3074247 p.His75Gln missense_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.78
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474291 c.285G>A synonymous_variant 0.93
rpoA 3878637 c.-130G>C upstream_gene_variant 0.22
rpoA 3878641 c.-134C>G upstream_gene_variant 0.25
clpC1 4040675 c.30C>G synonymous_variant 0.96
embC 4240409 p.Pro183Ala missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.1
embB 4246584 p.Arg24Pro missense_variant 0.19
aftB 4268619 p.Val73Gly missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0