TB-Profiler result

Run: ERR2228970
Summary

Run ID: ERR2228970

Sample name:

Date: 31-03-2023 16:28:47

Number of reads: 441100

Percentage reads mapped: 99.59

Strain: lineage4.8

Drug-resistance: RR-TB

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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
rpoB 761116 p.Asn437Ile missense_variant 0.12 rifampicin
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 5714 p.Lys159* stop_gained 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575505 p.His53Leu missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.18
ccsA 620366 p.Asn159Ser missense_variant 0.13
ccsA 620469 p.Ser193Arg missense_variant 0.15
rpoB 762456 p.Gly884Arg missense_variant 0.15
rpoB 763252 c.3448delG frameshift_variant 0.25
rpoC 763478 p.Arg37Ser missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775852 p.Ser877Gly missense_variant 0.13
mmpL5 776018 c.2463G>C synonymous_variant 0.25
mmpL5 776021 c.2460G>C synonymous_variant 0.25
mmpL5 777732 c.748dupC frameshift_variant 0.14
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
rrs 1473325 n.1480G>C non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.22
PPE35 2167868 c.2745A>C synonymous_variant 0.2
PPE35 2168238 p.Pro792Gln missense_variant 0.5
PPE35 2168477 c.2136C>A synonymous_variant 0.11
PPE35 2168500 p.Ser705Pro missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169935 c.678C>T synonymous_variant 0.25
Rv1979c 2221862 p.Arg435Cys missense_variant 0.15
Rv1979c 2222842 p.Val108Glu missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726371 p.Val60Ala missense_variant 0.2
ribD 2986698 c.-141G>A upstream_gene_variant 0.18
ribD 2986743 c.-96G>T upstream_gene_variant 0.17
ribD 2987263 p.Val142Glu missense_variant 0.12
ribD 2987454 p.Asp206Asn missense_variant 0.14
thyA 3074271 c.201C>G synonymous_variant 0.29
ald 3087150 p.Gly111Ser missense_variant 0.18
Rv3236c 3612631 p.Met162Ile missense_variant 0.2
alr 3840856 p.Arg189Gly missense_variant 0.14
rpoA 3877678 p.Ala277Glu missense_variant 0.2
clpC1 4038843 p.Val621Glu missense_variant 0.14
clpC1 4040291 c.414G>A synonymous_variant 0.18
embC 4240683 p.Asp274Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245456 p.Glu742Gln missense_variant 0.14
embB 4248783 p.Pro757His missense_variant 0.15
ethA 4326699 p.Arg259Cys missense_variant 0.11
ethA 4327713 c.-240A>C upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408431 c.-229G>A upstream_gene_variant 0.33
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0