TB-Profiler result

Run: ERR4423615
Summary

Run ID: ERR4423615

Sample name:

Date: 01-04-2023 05:55:26

Number of reads: 1597916

Percentage reads mapped: 84.48

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.2 Euro-American T;LAM RD726 0.98
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.98
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761108 p.Met434Ile missense_variant 0.17 rifampicin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2154864 c.1247dupT frameshift_variant 1.0 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 1.0 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247574 p.Asp354Ala 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 7293 c.-9G>A upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7819 p.Leu173Pro missense_variant 0.14
gyrA 8681 c.1380C>A synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620521 p.Ala211Ser missense_variant 0.14
rpoC 763426 c.57C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
mmpR5 779006 p.Gly6Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474026 n.369C>T non_coding_transcript_exon_variant 0.18
rrl 1474616 n.959G>T non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.2
inhA 1674578 p.Ser126Leu missense_variant 0.15
rpsA 1833674 p.Lys45Glu missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223298 c.-134C>T upstream_gene_variant 0.12
pncA 2289677 c.-436C>A upstream_gene_variant 0.15
eis 2714532 c.801C>A synonymous_variant 0.15
ribD 2986825 c.-14C>T upstream_gene_variant 0.17
Rv2752c 3064963 c.1228delG frameshift_variant 0.17
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3449592 c.1089C>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474271 p.Gln89* stop_gained 0.13
fprA 3474541 p.Ala179Thr missense_variant 0.14
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
rpoA 3878599 c.-92C>G upstream_gene_variant 0.11
panD 4043977 c.304delC frameshift_variant 0.18
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embA 4243783 p.Gly184Glu missense_variant 0.14
embA 4246371 p.Arg1047Ser missense_variant 0.12
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268526 p.Arg104Pro missense_variant 0.15
aftB 4268528 c.309C>T synonymous_variant 0.15
ethA 4326581 p.Asn298Ile missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0