TB-Profiler result

Run: ERR11068772

Summary

Run ID: ERR11068772

Sample name:

Date: 07-04-2023 01:16:33

Number of reads: 3440769

Percentage reads mapped: 99.62

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
embB 4247663 p.Tyr384Asn missense_variant 0.11 ethambutol
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
fgd1 491356 p.Phe192Ile missense_variant 0.11
mshA 576116 p.Ala257Pro missense_variant 0.29
mshA 576119 p.Ala258Pro missense_variant 0.5
ccsA 619807 c.-84G>A upstream_gene_variant 0.25
ccsA 619837 c.-54G>T upstream_gene_variant 0.18
ccsA 620094 c.204G>A synonymous_variant 0.17
rpoC 764342 p.Arg325Cys missense_variant 0.17
rpoC 766073 p.Ala902Thr missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304013 c.1083G>T synonymous_variant 0.14
fbiC 1305433 p.Ala835Thr missense_variant 0.17
Rv1258c 1407127 p.Arg72Cys missense_variant 0.18
Rv1258c 1407155 c.186C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674818 p.Ala206Val missense_variant 0.15
rpsA 1834852 c.1311C>G synonymous_variant 0.14
rpsA 1834869 p.Arg443His missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918064 p.Pro42Arg missense_variant 0.25
katG 2155739 p.Gly125Arg missense_variant 0.4
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288693 c.549T>C synonymous_variant 0.11
eis 2714891 p.Arg148Cys missense_variant 0.14
folC 2747714 c.-116G>A upstream_gene_variant 0.13
thyX 3067237 p.Asp237Asn missense_variant 0.2
thyX 3067387 p.Gly187Ser missense_variant 0.14
thyX 3067514 c.432C>T synonymous_variant 0.14
fbiD 3339312 c.195C>T synonymous_variant 0.5
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiB 3642234 p.Arg234Trp missense_variant 0.5
rpoA 3878552 c.-45C>A upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.19
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4241182 c.1320G>A synonymous_variant 0.11
embC 4242374 p.Arg838Trp missense_variant 0.11
embC 4242425 p.Arg855* stop_gained 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243892 c.660G>A synonymous_variant 0.11
embB 4247124 p.Ala204Val missense_variant 0.12
ethA 4328436 c.-963G>T upstream_gene_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