TB-Profiler result

Run: SRR3105804
Summary

Run ID: SRR3105804

Sample name:

Date: 04-04-2023 05:10:05

Number of reads: 1216565

Percentage reads mapped: 97.8

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 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155628 p.Ala162Thr missense_variant 0.23 isoniazid
katG 2156123 c.-12G>A upstream_gene_variant 0.71 isoniazid
pncA 2289040 p.Trp68Arg missense_variant 0.17 pyrazinamide
pncA 2289212 p.Gln10His missense_variant 0.12 pyrazinamide
embB 4247473 p.Phe320Leu missense_variant 1.0 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 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 619839 c.-52C>A upstream_gene_variant 0.14
ccsA 620748 c.858T>G synonymous_variant 0.36
rpoC 765515 p.Leu716Phe missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472504 n.659A>T non_coding_transcript_exon_variant 0.14
rrs 1472512 n.667A>G non_coding_transcript_exon_variant 0.35
inhA 1674952 p.Pro251Ala missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288869 p.Val125Leu missense_variant 0.28
folC 2747263 c.336C>A synonymous_variant 0.15
ribD 2986827 c.-12G>A upstream_gene_variant 0.96
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087584 c.765C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840431 c.990C>T synonymous_variant 1.0
clpC1 4039932 p.Gly258Val missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 1.0
ethR 4327691 p.Asp48Gly missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407790 p.Ala138Glu missense_variant 1.0