TB-Profiler result

Run: SRR14088366
Summary

Run ID: SRR14088366

Sample name:

Date: 03-04-2023 09:46:04

Number of reads: 1028839

Percentage reads mapped: 99.57

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
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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 7572 p.Ser91Pro missense_variant 0.2 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761086 p.Thr427Ile missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289253 c.-12T>C upstream_gene_variant 1.0 pyrazinamide
embB 4247495 p.Asp328Tyr missense_variant 1.0 ethambutol
ethA 4326350 c.1123delT frameshift_variant 0.58 ethionamide, ethionamide
gid 4408087 c.115delC frameshift_variant 1.0 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 5517 p.Ile93Lys missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Ser missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7873 p.Pro191Leu missense_variant 0.13
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
mshA 576108 p.Ala254Gly missense_variant 0.19
rpoB 761152 p.Leu449Gln missense_variant 0.19
rpoB 761489 c.1683G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776257 p.Ala742Thr missense_variant 0.12
mmpL5 777054 p.Glu476Gly missense_variant 0.17
mmpS5 779517 c.-612G>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781839 p.Arg94Cys missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103027 c.15delA frameshift_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168664 p.Thr650Arg missense_variant 0.18
PPE35 2169278 c.1335T>C synonymous_variant 0.25
PPE35 2169281 c.1332T>G synonymous_variant 0.25
PPE35 2169287 c.1326T>C synonymous_variant 0.25
PPE35 2169596 p.Phe339Trp missense_variant 0.18
PPE35 2169602 c.1011C>A synonymous_variant 0.15
PPE35 2169623 c.990T>C synonymous_variant 0.12
PPE35 2169732 p.Asn294Ser missense_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2222554 p.Pro204Leu missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517959 c.-156C>T upstream_gene_variant 0.29
ribD 2986827 c.-12G>A upstream_gene_variant 0.28
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
fbiD 3339734 p.Ala206Gly missense_variant 0.29
fbiD 3339746 p.Ala210Gly missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.95
rpoA 3877797 c.711G>T synonymous_variant 0.18
clpC1 4040041 p.Lys222Glu missense_variant 0.11
panD 4043902 p.Asn127Thr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268623 p.Trp72Gly missense_variant 0.25
ethA 4326323 p.Val384Gly missense_variant 0.27
ethA 4326393 p.Val361Leu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0