TB-Profiler result

Run: ERR4799050
Summary

Run ID: ERR4799050

Sample name:

Date: 01-04-2023 08:49:47

Number of reads: 5432705

Percentage reads mapped: 99.63

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 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.97
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.99
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 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288920 p.Gly108Arg missense_variant 0.99 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.99 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 0.98
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.2
mshA 576482 p.Val379Leu missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 0.98
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2168604 p.Pro670Leu missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.99
pncA 2289365 c.-125delC upstream_gene_variant 0.99
ahpC 2726105 c.-88G>A upstream_gene_variant 0.99
thyA 3074247 p.His75Gln missense_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474291 c.285G>A synonymous_variant 0.99
rpoA 3877949 p.Thr187Ala missense_variant 0.95
rpoA 3878637 c.-130G>C upstream_gene_variant 0.18
clpC1 4040675 c.30C>G synonymous_variant 0.98
embC 4242075 p.Arg738Gln missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4244741 c.1509C>T synonymous_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.44
ethA 4326368 p.Tyr369Cys missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0