TB-Profiler result

Run: ERR245799

Summary

Run ID: ERR245799

Sample name:

Date: 31-03-2023 18:21:39

Number of reads: 11692903

Percentage reads mapped: 99.4

Strain: lineage4.3.4.1

Drug-resistance: Sensitive


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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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
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 8445 p.Arg382Gly missense_variant 0.28
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.26
rpoB 759831 p.Thr9Pro missense_variant 0.26
rpoC 762836 c.-534C>G upstream_gene_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 0.99
rpoC 765082 c.1713G>C synonymous_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417501 c.-154A>C upstream_gene_variant 0.25
atpE 1461019 c.-26C>A upstream_gene_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.2
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.17
fabG1 1673449 p.Thr4Pro missense_variant 0.38
inhA 1674892 p.Asn231Asp missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.39
ndh 2102891 p.Phe51Ser missense_variant 0.24
PPE35 2169320 p.Leu431Phe missense_variant 0.16
PPE35 2169866 c.747G>C synonymous_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.3
eis 2715586 c.-254G>C upstream_gene_variant 0.65
ahpC 2725954 c.-239C>T upstream_gene_variant 0.3
pepQ 2859381 c.1038C>G synonymous_variant 0.23
Rv2752c 3064552 p.Arg547Pro missense_variant 0.17
Rv2752c 3064741 p.Gly484Ala missense_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.24
Rv3083 3449673 p.Tyr390* stop_gained 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.23
fprA 3475280 p.Val425Gly missense_variant 0.24
Rv3236c 3611982 p.Ala379Pro missense_variant 0.35
Rv3236c 3611992 c.1125T>G synonymous_variant 0.37
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3640614 c.-921C>T upstream_gene_variant 1.0
fbiB 3642734 c.1200G>C synonymous_variant 0.19
ddn 3987013 p.Gly57Ala missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.22
clpC1 4039363 p.Ala448Pro missense_variant 0.21
clpC1 4039932 p.Gly258Val missense_variant 0.24
embC 4239842 c.-21C>A upstream_gene_variant 0.14
embC 4241128 c.1266G>C synonymous_variant 0.21
embC 4241429 p.Phe523Val missense_variant 0.64
embC 4241456 p.Ala532Pro missense_variant 0.42
embC 4242476 p.Pro872Ala missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.3
embC 4242827 p.Leu989Val missense_variant 0.18
embA 4245329 c.2097A>G synonymous_variant 0.99
embB 4249504 p.Gln997His missense_variant 0.18
aftB 4268812 p.Ser9Ala missense_variant 0.24
aftB 4269411 c.-575T>C upstream_gene_variant 0.99
ubiA 4269529 p.Ala102Gly missense_variant 0.23
ethA 4327672 c.-199G>A upstream_gene_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0