TB-Profiler result

Run: SRR22175186

Summary

Run ID: SRR22175186

Sample name:

Date: 04-04-2023 03:59:46

Number of reads: 771551

Percentage reads mapped: 99.22

Strain: lineage3

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 1.0
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 1.0 rifampicin
rpoC 764948 p.Leu527Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.94 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.12 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
thyA 3067988 c.-2232_*5691del transcript_ablation 1.0 para-aminosalicylic_acid
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 7301 c.-1G>T upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.94
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 0.11
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
atpE 1460857 c.-188C>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472051 n.206A>G non_coding_transcript_exon_variant 0.18
rrl 1475720 n.2063A>G non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155707 p.Trp135Cys missense_variant 0.11
PPE35 2167828 p.Ala929Thr missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.92
ahpC 2726105 c.-88G>A upstream_gene_variant 0.95
ahpC 2726431 p.Ala80Gly missense_variant 0.15
Rv2752c 3065008 p.Pro395Leu missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474718 p.Ala238Thr missense_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878455 p.Arg18Gln missense_variant 0.15
rpoA 3878595 c.-88C>A upstream_gene_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245274 p.Arg681Leu missense_variant 0.12
ethA 4327038 p.Gly146Cys missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408335 c.-133A>G upstream_gene_variant 1.0