TB-Profiler result

Run: ERR7361969
Summary

Run ID: ERR7361969

Sample name:

Date: 02-04-2023 04:14:36

Number of reads: 1604855

Percentage reads mapped: 99.71

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288719 p.Met175Val missense_variant 1.0 pyrazinamide
alr 3840393 p.Met343Thr missense_variant 1.0 cycloserine
embB 4247429 p.Met306Val 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
gyrB 5809 c.570C>T synonymous_variant 0.17
gyrB 6464 p.Lys409Glu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 760001 c.195C>A synonymous_variant 0.22
rpoB 760035 p.Val77Met missense_variant 0.15
rpoC 763494 p.Glu42Gly missense_variant 0.22
rpoC 763796 p.Met143Val missense_variant 0.11
rpoC 764014 c.645G>A synonymous_variant 0.13
rpoC 765797 p.Asn810Asp missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781912 p.Gly118Val missense_variant 0.13
rplC 800929 p.Thr41Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471843 n.-3G>T upstream_gene_variant 1.0
rrs 1472609 n.764G>T non_coding_transcript_exon_variant 0.29
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474391 n.734G>T non_coding_transcript_exon_variant 0.14
inhA 1674463 p.Leu88Phe missense_variant 0.15
rpsA 1833489 c.-53T>A upstream_gene_variant 0.17
rpsA 1834132 c.591G>A synonymous_variant 0.22
rpsA 1834270 c.729G>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154240 p.Met624Ile missense_variant 0.17
katG 2155605 c.507C>A synonymous_variant 0.15
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169122 c.1491C>G synonymous_variant 0.15
PPE35 2169149 c.1464G>C synonymous_variant 1.0
PPE35 2169345 p.Asn423Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288949 p.Ala98Val missense_variant 1.0
pncA 2289608 c.-367A>G upstream_gene_variant 0.2
kasA 2518106 c.-9C>A upstream_gene_variant 0.15
pepQ 2860337 p.Ile28Leu missense_variant 0.17
thyX 3067720 p.Ala76Thr missense_variant 0.12
fbiB 3642835 p.Gly434Glu missense_variant 0.12
rpoA 3877486 p.Tyr341Cys missense_variant 0.1
rpoA 3878531 c.-25delG upstream_gene_variant 0.25
clpC1 4039729 p.Asp326Asn missense_variant 1.0
panD 4044285 c.-4A>G upstream_gene_variant 0.29
embC 4242097 c.2237delG frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269518 p.Ala106Pro missense_variant 0.1
ethR 4327123 c.-426G>A upstream_gene_variant 0.12
ethR 4327465 c.-84C>T upstream_gene_variant 0.22
ethA 4327545 c.-72G>A upstream_gene_variant 0.12
ethR 4327907 p.Val120Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0
ethA 4326539 c.866_934delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT disruptive_inframe_deletion 1.0