TB-Profiler result

Run: ERR2229221
Summary

Run ID: ERR2229221

Sample name:

Date: 31-03-2023 16:49:22

Number of reads: 416751

Percentage reads mapped: 99.63

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 7362 p.Glu21Gln missense_variant 1.0
mshA 576562 c.1215G>C synonymous_variant 0.2
ccsA 620571 c.681A>C synonymous_variant 0.5
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoC 763987 c.618C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781893 p.Gln112Lys missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304772 p.Tyr614* stop_gained 0.17
fbiC 1305204 c.2274C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473489 n.-169C>A upstream_gene_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.25
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918518 c.579C>A synonymous_variant 0.12
ndh 2101897 c.1146C>T synonymous_variant 0.12
ndh 2102641 c.402C>T synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.13
PPE35 2170247 p.Ile122Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.22
ahpC 2726645 c.453C>T synonymous_variant 0.2
ahpC 2726740 p.Pro183Leu missense_variant 0.14
folC 2746455 c.1144C>T synonymous_variant 0.17
pepQ 2859744 c.675G>A synonymous_variant 0.25
ribD 2987182 p.Pro115Leu missense_variant 0.5
ribD 2987253 p.Ala139Thr missense_variant 0.29
Rv2752c 3064583 p.Val537Ile missense_variant 0.15
Rv2752c 3065847 c.345A>G synonymous_variant 0.29
ald 3086756 c.-64A>T upstream_gene_variant 0.13
fprA 3474435 c.429C>T synonymous_variant 0.33
fbiB 3640833 c.-702G>A upstream_gene_variant 0.13
alr 3841364 c.56delG frameshift_variant 0.12
rpoA 3878085 p.Glu141Asp missense_variant 0.15
clpC1 4040761 c.-57G>A upstream_gene_variant 0.17
embC 4242542 p.Arg894Cys missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245372 p.Pro714Ser missense_variant 0.2
embA 4245967 p.Phe912Ser 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
ethR 4327369 c.-180C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0