TB-Profiler result

Run: ERR2229701
Summary

Run ID: ERR2229701

Sample name:

Date: 31-03-2023 17:26:57

Number of reads: 1201449

Percentage reads mapped: 99.14

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 7237 c.-65C>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491644 p.Ser288Pro missense_variant 0.14
mshA 575694 p.Pro116His missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576313 c.967delG frameshift_variant 0.17
mshA 576607 c.1260G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304746 p.Asp606Asn missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475453 n.1796T>A non_coding_transcript_exon_variant 0.29
rrl 1475887 n.2230G>A non_coding_transcript_exon_variant 0.29
rrl 1476212 n.2555T>A non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
inhA 1673851 c.-351A>G upstream_gene_variant 0.11
tlyA 1917822 c.-118G>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102861 p.Gly61Val missense_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.23
PPE35 2169287 c.1326T>C synonymous_variant 0.23
PPE35 2169293 c.1320T>C synonymous_variant 0.13
PPE35 2169308 c.1305C>T synonymous_variant 0.17
PPE35 2169397 p.Gly406Ser missense_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.75
PPE35 2170053 p.Thr187Ser missense_variant 0.76
PPE35 2170159 p.Ala152Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289955 c.-714C>T upstream_gene_variant 0.13
pncA 2290066 c.-825G>A upstream_gene_variant 0.15
kasA 2518833 p.Gly240Val missense_variant 0.11
kasA 2519189 p.Val359Leu missense_variant 0.17
Rv2752c 3066077 p.Arg39* stop_gained 0.11
thyX 3067551 p.Leu132Gln missense_variant 0.18
fprA 3474114 c.108C>T synonymous_variant 0.14
Rv3236c 3612883 c.234T>A synonymous_variant 0.13
fbiB 3642521 p.Asp329Glu missense_variant 0.17
fbiB 3642842 c.1308C>T synonymous_variant 0.18
alr 3840484 p.Gly313Arg missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.21
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4039653 p.Thr351Met missense_variant 0.13
clpC1 4039691 c.1014G>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244860 p.Gly543Val missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4248817 p.Asp768Glu missense_variant 0.14
aftB 4268582 c.255C>T synonymous_variant 0.17
ethA 4327346 p.Gly43Ala missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0