TB-Profiler result

Run: SRR22175173
Summary

Run ID: SRR22175173

Sample name:

Date: 04-04-2023 03:58:53

Number of reads: 1709805

Percentage reads mapped: 99.34

Strain: lineage4.2.2.2

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
lineage4 Euro-American LAM;T;S;X;H None 0.99
lineage4.2 Euro-American H;T;LAM None 0.97
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.97
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.94
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 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155289 p.Thr275Ala missense_variant 1.0 isoniazid
embB 4247729 p.Gly406Ser missense_variant 0.94 ethambutol
gid 4408100 c.102delG frameshift_variant 0.9 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 5965 c.726A>G synonymous_variant 0.81
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.92
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9328 p.Ala676Val missense_variant 0.84
fgd1 491742 c.960T>C synonymous_variant 0.19
mshA 576077 c.730C>T synonymous_variant 0.9
rpoB 761489 c.1683G>A synonymous_variant 0.97
rpoB 762888 p.His1028Tyr missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305180 c.2250G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.87
rpsA 1834177 c.636A>C synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289290 c.-49C>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.98
ald 3086742 c.-78A>C upstream_gene_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338513 c.9C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.12