TB-Profiler result

Run: ERR2229239
Summary

Run ID: ERR2229239

Sample name:

Date: 31-03-2023 16:51:30

Number of reads: 1092625

Percentage reads mapped: 99.16

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 7186 c.-116C>G upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576111 p.Ala255Gly missense_variant 0.29
mshA 576243 p.Gly299Asp missense_variant 0.12
ccsA 620080 p.Val64Met missense_variant 0.15
rpoC 765754 c.2385C>T synonymous_variant 0.18
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673966 p.Val176Ala missense_variant 0.11
inhA 1674431 p.Arg77Gln missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155450 p.Ala221Asp missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.32
PPE35 2170053 p.Thr187Ser missense_variant 0.36
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170157 p.Ala152Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223324 c.-160G>A upstream_gene_variant 0.12
pncA 2289776 c.-535C>T upstream_gene_variant 0.17
pncA 2290044 c.-803G>C upstream_gene_variant 0.2
kasA 2518879 c.765A>G synonymous_variant 0.12
kasA 2519173 c.1059C>G synonymous_variant 0.23
eis 2715057 c.276C>T synonymous_variant 0.15
eis 2715060 p.His91Met missense_variant 0.15
eis 2715065 p.Thr90Ala missense_variant 0.17
pepQ 2859991 p.Leu143Pro missense_variant 0.14
Rv2752c 3064788 p.Leu468Phe missense_variant 0.12
fbiD 3339500 p.Ala128Val missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.23
alr 3841612 c.-193_-192insC upstream_gene_variant 0.15
rpoA 3878567 c.-60C>G upstream_gene_variant 0.67
rpoA 3878569 c.-63_-62insG upstream_gene_variant 1.0
clpC1 4039803 p.Ala301Gly missense_variant 0.11
clpC1 4039829 p.Leu292Ile missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244424 p.Arg398Trp missense_variant 0.22
embA 4245069 p.Val613Met missense_variant 0.13
embB 4246567 c.54_55insT frameshift_variant 0.29
aftB 4267954 p.Ala295Pro missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0