TB-Profiler result

Run: ERR10796567
Summary

Run ID: ERR10796567

Sample name:

Date: 31-03-2023 11:11:39

Number of reads: 4994484

Percentage reads mapped: 100.0

Strain: lineage4.3.4.2

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
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 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
gyrB 5791 c.552A>G synonymous_variant 0.11
gyrA 6817 c.-485G>A upstream_gene_variant 1.0
gyrB 6980 p.Ala581Thr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491460 p.Asp226Glu missense_variant 0.15
ccsA 620236 p.Leu116Met missense_variant 0.22
ccsA 620535 p.Met215Ile missense_variant 0.11
ccsA 620826 c.936G>T synonymous_variant 0.14
rpoB 761837 c.2031C>T synonymous_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766502 p.Pro1045Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778167 p.Ala105Asp missense_variant 0.17
mmpR5 778439 c.-551C>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407087 p.Ala85Val missense_variant 0.12
Rv1258c 1407109 p.Ala78Thr missense_variant 0.13
embR 1416708 p.Ala214Thr missense_variant 0.15
atpE 1460872 c.-173G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473651 n.-7G>T upstream_gene_variant 0.11
rrl 1473785 n.128C>A non_coding_transcript_exon_variant 0.12
rrl 1476045 n.2388G>A non_coding_transcript_exon_variant 0.14
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.29
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.45
rrl 1476393 n.2736C>T non_coding_transcript_exon_variant 0.42
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.25
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
inhA 1674604 c.403C>T synonymous_variant 0.13
rpsA 1833390 c.-152T>C upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155001 p.Pro371Thr missense_variant 0.14
PPE35 2169670 p.Gly315Cys missense_variant 0.27
PPE35 2169714 p.Gly300Val missense_variant 0.17
PPE35 2170470 p.Val48Ala missense_variant 0.12
PPE35 2170583 c.30C>T synonymous_variant 0.14
Rv1979c 2221761 p.Tyr468* stop_gained 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067915 p.Leu11Met missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074193 c.279C>A synonymous_variant 0.13
thyA 3074520 c.-49G>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448349 c.-155C>T upstream_gene_variant 0.2
Rv3083 3448467 c.-37T>C upstream_gene_variant 0.15
Rv3083 3448985 p.Gly161Val missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3841567 c.-147A>G upstream_gene_variant 0.11
rpoA 3877596 c.912G>T synonymous_variant 0.13
rpoA 3878474 p.Asp12Tyr missense_variant 0.15
ddn 3987003 p.Arg54Cys missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4240125 p.Cys88Tyr missense_variant 0.14
embC 4240812 p.Phe317Ser missense_variant 0.17
embC 4242242 p.Val794Ile missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243813 p.Arg194Gln missense_variant 1.0
embA 4244729 c.1497C>T synonymous_variant 0.17
embA 4245866 p.Trp878Cys missense_variant 0.2
embB 4248569 p.Leu686Met missense_variant 0.12
embB 4248779 p.Glu756Lys missense_variant 0.12
aftB 4269024 c.-188G>T upstream_gene_variant 0.33
ubiA 4269432 p.Met134Ile missense_variant 0.12
ubiA 4269542 p.Pro98Ser missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0