TB-Profiler result

Run: ERR4821710
Summary

Run ID: ERR4821710

Sample name:

Date: 01-04-2023 17:24:30

Number of reads: 381949

Percentage reads mapped: 98.46

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 0.99
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.67 streptomycin
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
gyrA 9609 p.Asp770Tyr missense_variant 0.22
fgd1 491778 p.Leu332Phe missense_variant 0.2
rpoC 764035 c.666C>A synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302817 c.-114C>A upstream_gene_variant 1.0
atpE 1460969 c.-76G>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
inhA 1674940 p.Ser247Pro missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167911 p.Ala901Gly missense_variant 0.5
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169504 p.Gly370Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726294 p.Tyr34* stop_gained 0.25
pepQ 2859601 c.817delG frameshift_variant 0.18
Rv2752c 3065395 p.Met266Thr missense_variant 0.22
ald 3086879 c.60G>A synonymous_variant 0.12
Rv3083 3448335 c.-169C>T upstream_gene_variant 0.14
fprA 3474038 p.Ser11Phe missense_variant 0.11
fprA 3474363 c.357G>A synonymous_variant 0.15
Rv3236c 3612448 c.669G>T synonymous_variant 1.0
alr 3840954 p.Val156Ala missense_variant 0.11
clpC1 4040764 c.-60A>G upstream_gene_variant 0.29
embC 4241069 p.Ala403Pro missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248336 p.Ala608Glu missense_variant 0.12
embB 4249253 p.Gly914Trp 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