TB-Profiler result

Run: ERR046785
Summary

Run ID: ERR046785

Sample name:

Date: 31-03-2023 08:51:04

Number of reads: 6752705

Percentage reads mapped: 97.97

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 0.99 rifampicin
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 9304 p.Gly668Asp missense_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.18
mshA 576751 p.Lys468Asn missense_variant 0.2
rpoB 759620 c.-187A>C upstream_gene_variant 0.29
rpoC 762836 c.-534C>G upstream_gene_variant 0.2
rpoC 764725 p.Phe452Leu missense_variant 0.31
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303601 p.Glu224Gly missense_variant 1.0
Rv1258c 1406358 p.Ile328Thr missense_variant 0.18
Rv1258c 1406750 c.591C>A synonymous_variant 0.17
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.16
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.23
PPE35 2167871 c.2742G>C synonymous_variant 0.2
PPE35 2169866 c.747G>C synonymous_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.25
eis 2715586 c.-254G>C upstream_gene_variant 0.33
folC 2746186 c.1413G>C synonymous_variant 0.15
pepQ 2859381 c.1038C>G synonymous_variant 0.21
Rv2752c 3064552 p.Arg547Pro missense_variant 0.15
Rv2752c 3064741 p.Gly484Ala missense_variant 0.3
Rv2752c 3065618 p.Gly192Arg missense_variant 0.16
thyX 3067995 c.-50A>C upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474601 p.Arg199Gly missense_variant 0.25
fbiB 3641955 p.Gly141Arg missense_variant 0.15
fbiB 3642734 c.1200G>C synonymous_variant 0.19
alr 3840268 p.Thr385Pro missense_variant 0.27
rpoA 3878238 p.Asp90Glu missense_variant 0.14
ddn 3987013 p.Gly57Ala missense_variant 0.25
clpC1 4038857 c.1848C>A synonymous_variant 0.17
clpC1 4039932 p.Gly258Val missense_variant 0.18
embC 4241056 c.1194C>G synonymous_variant 0.22
embC 4242425 p.Arg855Gly missense_variant 0.12
embC 4242476 p.Pro872Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.2
embC 4242827 p.Leu989Val missense_variant 0.15
embA 4243977 p.Ala249Pro missense_variant 0.26
embB 4248725 p.Ser738Ala missense_variant 0.22
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.3
aftB 4269540 c.-704C>T upstream_gene_variant 0.99
ethA 4327672 c.-199G>A upstream_gene_variant 0.25
ethR 4327912 p.Arg122Gly missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0