TB-Profiler result

Run: ERR4407473
Summary

Run ID: ERR4407473

Sample name:

Date: 01-04-2023 05:45:35

Number of reads: 279736

Percentage reads mapped: 99.52

Strain: lineage4.3.4

Drug-resistance: HR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM 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
katG 2155433 c.678delG frameshift_variant 0.18 isoniazid
embB 4247730 p.Gly406Ala 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 5156 c.-84G>A upstream_gene_variant 0.1
gyrB 5269 c.30C>T synonymous_variant 0.15
gyrB 5632 c.393A>G synonymous_variant 1.0
gyrB 6059 p.Ser274Gly missense_variant 1.0
gyrA 6817 c.-485G>A upstream_gene_variant 1.0
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 491050 p.Phe90Leu missense_variant 0.12
rpoB 759663 c.-144G>A upstream_gene_variant 0.33
rpoB 761152 p.Leu449Gln missense_variant 0.17
rpoB 761340 p.Lys512Glu missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460913 c.-132G>C upstream_gene_variant 0.25
atpE 1461143 c.99C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472318 n.473A>G non_coding_transcript_exon_variant 0.18
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.14
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.11
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.1
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.1
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.1
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.1
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.1
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.1
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.1
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.11
rrs 1472714 n.872_873delCC non_coding_transcript_exon_variant 0.12
rrs 1472934 n.1089C>T non_coding_transcript_exon_variant 0.14
rrl 1473440 n.-217delT upstream_gene_variant 0.11
rrl 1474364 n.707G>A non_coding_transcript_exon_variant 0.12
rrl 1474921 n.1268dupG non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102072 p.Ala324Val missense_variant 0.1
katG 2155024 p.Thr363Ile missense_variant 0.15
PPE35 2168717 c.1896G>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859431 c.988T>C synonymous_variant 0.1
pepQ 2860317 c.102A>G synonymous_variant 0.12
Rv2752c 3064721 p.His491Tyr missense_variant 0.5
Rv2752c 3064928 c.1264T>C synonymous_variant 0.12
Rv2752c 3065188 p.Val335Ala missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339537 c.420C>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474672 p.Asp222Glu missense_variant 0.12
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612472 c.645C>T synonymous_variant 0.22
fbiB 3642320 c.786C>A synonymous_variant 0.2
alr 3840444 p.Leu326Pro missense_variant 0.1
alr 3841470 c.-50G>A upstream_gene_variant 0.1
rpoA 3877508 p.Gly334Cys missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040030 c.675C>A synonymous_variant 0.12
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4240838 c.978delG frameshift_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243487 c.255C>T synonymous_variant 0.13
embA 4244907 p.Gly559Ser missense_variant 0.2
embA 4246111 p.Arg960Gln missense_variant 0.11
embA 4246480 p.Gly1083Asp missense_variant 0.18
embB 4247176 c.663G>A synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407974 p.Val77Met missense_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0