TB-Profiler result

Run: ERR046789
Summary

Run ID: ERR046789

Sample name:

Date: 31-03-2023 08:50:55

Number of reads: 2410805

Percentage reads mapped: 96.98

Strain: lineage4.1.1.3.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 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 761277 p.Ile491Phe missense_variant 1.0 rifampicin
katG 2154695 p.Val473Phe missense_variant 0.53 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408100 c.102delG 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.498A>C synonymous_variant 0.23
gyrA 8377 p.Asp359Gly missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.3
rpoC 762836 c.-534C>G upstream_gene_variant 0.21
rpoC 764725 p.Phe452Leu missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779371 p.Ala128Pro missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.16
fbiC 1303016 p.Val29Gly missense_variant 0.17
fbiC 1303601 p.Glu224Gly missense_variant 1.0
embR 1416480 p.Ala290Pro missense_variant 0.14
atpE 1461019 c.-26C>A upstream_gene_variant 0.23
rrs 1471658 n.-188T>G upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.1
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.1
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.15
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.11
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.1
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.11
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
inhA 1674892 p.Asn231Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.21
katG 2156110 p.Val1Gly missense_variant 0.28
PPE35 2169866 c.747G>C synonymous_variant 0.54
PPE35 2170156 p.Ala153Pro missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.32
folC 2747218 p.Ile127Met missense_variant 0.18
pepQ 2859381 c.1038C>G synonymous_variant 0.38
Rv2752c 3064552 p.Arg547Pro missense_variant 0.19
Rv2752c 3064741 p.Gly484Ala missense_variant 0.32
thyX 3067995 c.-50A>C upstream_gene_variant 0.27
thyA 3073806 c.666C>G synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.29
fbiD 3339733 p.Ala206Pro missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.23
fbiA 3641411 p.Val290Gly missense_variant 0.24
fbiB 3642734 c.1200G>C synonymous_variant 0.14
alr 3840268 p.Thr385Pro missense_variant 0.24
rpoA 3878641 c.-134C>G upstream_gene_variant 0.25
clpC1 4038857 c.1848C>A synonymous_variant 0.24
clpC1 4039363 p.Ala448Pro missense_variant 0.23
clpC1 4039931 p.Gly258Val missense_variant 0.15
embC 4241456 p.Ala532Pro missense_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243977 p.Ala249Pro missense_variant 0.27
embB 4248725 p.Ser738Ala missense_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.16
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.22
ethR 4327912 p.Arg122Gly missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0