TB-Profiler result

Run: ERR4820299

Summary

Run ID: ERR4820299

Sample name:

Date: 01-04-2023 16:36:09

Number of reads: 578587

Percentage reads mapped: 98.4

Strain: lineage4.1.1.3

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
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 5459 p.Gly74Cys missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7640 c.339G>A synonymous_variant 0.22
gyrA 8021 c.720C>T synonymous_variant 0.5
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9774 p.Asp825Asn missense_variant 0.11
mshA 575821 c.474G>C synonymous_variant 0.17
ccsA 620242 c.353delG frameshift_variant 0.13
ccsA 620551 p.Asp221Tyr missense_variant 0.12
ccsA 620691 c.801G>A synonymous_variant 0.22
rpoB 761749 p.Ser648Leu missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776545 p.Lys646Glu missense_variant 0.25
mmpL5 778063 p.Gln140Lys missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781566 p.Thr3Ser missense_variant 0.33
rplC 800738 c.-71T>C upstream_gene_variant 0.13
fbiC 1303423 c.497dupG frameshift_variant 0.11
fbiC 1304924 p.Pro665Gln missense_variant 0.29
Rv1258c 1406400 c.940dupA frameshift_variant 0.33
Rv1258c 1406794 p.Leu183Met missense_variant 0.12
embR 1416756 p.Thr198Ala missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rrl 1476483 n.2826G>T non_coding_transcript_exon_variant 0.33
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.4
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.5
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.5
inhA 1674576 c.375T>C synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102459 p.His195Arg missense_variant 1.0
katG 2154882 c.1230G>A synonymous_variant 0.25
katG 2155553 p.Arg187Trp missense_variant 0.25
katG 2156086 p.Thr9Ile missense_variant 0.25
PPE35 2169054 p.Ala520Asp missense_variant 0.13
PPE35 2170307 c.306G>T synonymous_variant 0.17
PPE35 2170698 c.-86G>C upstream_gene_variant 0.12
Rv1979c 2222285 p.Ala294Thr missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223314 c.-150C>A upstream_gene_variant 0.25
ahpC 2726010 c.-182_-181delCT upstream_gene_variant 0.15
ahpC 2726771 c.579T>C synonymous_variant 0.15
folC 2746622 p.Val326Ala missense_variant 0.12
pepQ 2859783 c.636G>C synonymous_variant 0.1
pepQ 2860154 p.Glu89Gln missense_variant 0.12
ribD 2986837 c.-2T>C upstream_gene_variant 0.2
ribD 2986897 p.Val20Ala missense_variant 0.12
ribD 2987322 c.485delT frameshift_variant 0.17
thyX 3067983 c.-38G>A upstream_gene_variant 0.12
thyA 3074594 c.-123C>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612220 c.897T>C synonymous_variant 0.2
Rv3236c 3612634 c.483G>A synonymous_variant 0.14
fbiA 3640849 p.Glu103Gln missense_variant 0.2
fbiB 3641704 p.Glu57Gly missense_variant 0.12
rpoA 3877952 p.Arg186Cys missense_variant 0.29
rpoA 3878231 p.Val93Ile missense_variant 0.13
rpoA 3878257 p.Val84Ala missense_variant 0.13
ddn 3987096 p.Asn85Tyr missense_variant 0.12
clpC1 4039684 p.Arg341Cys missense_variant 0.25
embC 4241495 p.Ala545Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244045 c.813G>A synonymous_variant 0.1
embB 4248220 c.1709delC frameshift_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249569 p.Ser1019* stop_gained 0.2
aftB 4267559 c.1278C>T synonymous_variant 0.2
ubiA 4269443 p.Tyr131His missense_variant 0.25
ethA 4326167 p.Pro436Gln missense_variant 0.25
ethA 4326206 p.Gly423Val missense_variant 0.2
ethA 4327278 p.Phe66Leu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338620 c.-99G>T upstream_gene_variant 0.25
whiB6 4338683 c.-162G>T upstream_gene_variant 0.25
gid 4408124 p.Ala27Pro missense_variant 0.4