TB-Profiler result

Run: ERR4819792
Summary

Run ID: ERR4819792

Sample name:

Date: 01-04-2023 16:18:32

Number of reads: 817276

Percentage reads mapped: 99.2

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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.67 streptomycin
gid 4408100 c.102delG frameshift_variant 1.0 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
gyrB 6965 p.Ser576Gly missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9124 p.Ile608Ser missense_variant 0.17
rpoB 759668 c.-139A>T upstream_gene_variant 0.13
rpoB 760782 p.Thr326Ala missense_variant 0.12
rpoB 762912 p.His1036Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801150 c.342G>A synonymous_variant 0.13
atpE 1460883 c.-162G>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471664 n.-182C>A upstream_gene_variant 0.2
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.5
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.67
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.67
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.67
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.67
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.67
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065519 p.Leu225Val missense_variant 0.13
thyX 3067589 c.357G>A synonymous_variant 0.12
alr 3841477 c.-57G>A upstream_gene_variant 0.11
clpC1 4038174 p.Glu844Gly missense_variant 0.1
clpC1 4038929 c.1776G>A synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.15
aftB 4266976 c.1860delG frameshift_variant 0.17
aftB 4267094 c.1742delC frameshift_variant 0.2
aftB 4268601 p.Leu79Pro missense_variant 1.0
ubiA 4269085 p.Val250Ala missense_variant 0.13
ethR 4327660 p.Glu38Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0