TB-Profiler result

Run: ERR2229478
Summary

Run ID: ERR2229478

Sample name:

Date: 31-03-2023 17:14:05

Number of reads: 616459

Percentage reads mapped: 99.43

Strain: lineage4.8

Drug-resistance: Other

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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
ethA 4326880 c.593delG frameshift_variant 0.18 ethionamide
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 5874 p.Arg212Thr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576173 p.Pro276Ser missense_variant 0.33
ccsA 620543 p.Arg218Gln missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781679 c.120C>T synonymous_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406174 p.Cys389Trp missense_variant 0.2
atpE 1460917 c.-128C>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473466 n.-192G>C upstream_gene_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475914 n.2257C>A non_coding_transcript_exon_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
fabG1 1673884 p.Asn149Asp missense_variant 0.11
rpsA 1834698 p.Glu386Gly missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102604 c.439T>C synonymous_variant 0.21
ndh 2102610 c.433T>C synonymous_variant 0.2
katG 2154232 p.Leu627Gln missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2169910 p.Asn235Tyr missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2223159 c.6C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289319 c.-78C>A upstream_gene_variant 0.12
kasA 2518606 c.492G>C synonymous_variant 0.22
kasA 2518809 p.Lys232Arg missense_variant 0.17
kasA 2519193 p.Leu360Arg missense_variant 0.29
ahpC 2725938 c.-255_-254insA upstream_gene_variant 0.15
ribD 2986677 c.-162G>T upstream_gene_variant 0.12
ribD 2986934 c.96C>T synonymous_variant 0.2
Rv2752c 3065539 p.Val218Ala missense_variant 0.11
Rv2752c 3067154 c.-963G>T upstream_gene_variant 0.11
thyX 3067610 p.Lys112Asn missense_variant 0.17
ald 3087139 p.Leu107Ser missense_variant 0.12
fprA 3473901 c.-106G>A upstream_gene_variant 0.13
fprA 3473920 c.-87G>T upstream_gene_variant 0.13
fprA 3474007 c.1A>C initiator_codon_variant 0.17
fprA 3475012 p.Asp336Asn missense_variant 0.14
fbiB 3641712 p.Leu60Val missense_variant 0.15
fbiB 3642422 c.888A>T synonymous_variant 0.25
ddn 3987201 p.Ala120Thr missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247512 c.999T>C synonymous_variant 0.13
embB 4247516 p.Asn335Asp missense_variant 0.14
embB 4247915 p.Arg468Cys missense_variant 0.15
embB 4248138 p.Gly542Asp missense_variant 0.11
embB 4248586 c.2073C>A synonymous_variant 0.13
embB 4248686 p.Gly725Trp missense_variant 0.2
embB 4249346 p.Ala945Thr missense_variant 0.18
aftB 4267671 p.Ala389Val missense_variant 0.12
aftB 4268788 p.Phe17Ile missense_variant 0.29
ethR 4327571 p.Gln8Leu missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407913 p.Arg97His missense_variant 0.14
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0