TB-Profiler result

Run: ERR4799919
Summary

Run ID: ERR4799919

Sample name:

Date: 01-04-2023 09:27:59

Number of reads: 3540788

Percentage reads mapped: 99.55

Strain: lineage4.2.2.2;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 0.5
lineage4 Euro-American LAM;T;S;X;H None 0.49
lineage4.2 Euro-American H;T;LAM None 0.5
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.52
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.44
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.48
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.45
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 7581 p.Asp94Asn missense_variant 0.55 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.56 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.38 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.63 isoniazid
pncA 2289155 c.86delG frameshift_variant 0.53 pyrazinamide
folC 2747480 p.Glu40Gly missense_variant 0.52 para-aminosalicylic_acid
embB 4247730 p.Gly406Ala missense_variant 0.43 ethambutol
ethA 4327045 p.Tyr143* stop_gained 0.45 ethionamide
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 7481 c.180C>T synonymous_variant 0.52
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.44
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.46
mshA 576077 c.730C>T synonymous_variant 0.41
rpoB 759746 c.-61C>T upstream_gene_variant 0.39
rpoB 761489 c.1683G>A synonymous_variant 0.37
rpoC 762434 c.-936T>G upstream_gene_variant 0.54
rpoC 763031 c.-339T>C upstream_gene_variant 0.5
rpoC 763923 p.Glu185Val missense_variant 0.49
rpoC 767123 p.Val1252Met missense_variant 0.41
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.49
mmpL5 776585 c.1896C>T synonymous_variant 0.53
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406242 p.Ala367Thr missense_variant 0.49
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 0.44
katG 2154724 p.Arg463Leu missense_variant 0.47
PPE35 2167926 p.Leu896Ser missense_variant 0.52
PPE35 2168604 p.Pro670Leu missense_variant 0.58
PPE35 2169634 p.Ala327Thr missense_variant 0.54
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.53
pncA 2289365 c.-125delC upstream_gene_variant 0.6
eis 2714888 p.Phe149Val missense_variant 0.43
ahpC 2726105 c.-88G>A upstream_gene_variant 0.47
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.34
ald 3086742 c.-78A>C upstream_gene_variant 0.69
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449404 c.902_904dupCCA disruptive_inframe_insertion 0.43
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240327 c.465G>A synonymous_variant 0.48
embC 4242075 p.Arg738Gln missense_variant 0.56
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269721 p.Ala38Val missense_variant 0.47
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.44
gid 4408273 c.-71C>T upstream_gene_variant 0.43