TB-Profiler result

Run: ERR4817262
Summary

Run ID: ERR4817262

Sample name:

Date: 01-04-2023 14:53:38

Number of reads: 822780

Percentage reads mapped: 99.19

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
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
gyrA 6433 c.-869C>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8170 p.Gln290Arg missense_variant 0.15
gyrA 8564 c.1263G>A synonymous_variant 0.12
rpoC 765811 c.2443_2444delCG frameshift_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779063 p.Gly25Asp missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781602 p.Lys15Glu missense_variant 0.15
atpE 1460883 c.-162G>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.67
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.5
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.5
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673560 p.Lys41Leu missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918175 p.Ile79Asn missense_variant 0.1
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860279 p.Ala47Val missense_variant 0.15
Rv2752c 3065444 p.Asp250Tyr missense_variant 0.15
ald 3086773 c.-47A>G upstream_gene_variant 0.12
fbiD 3339420 c.303C>T synonymous_variant 0.14
rpoA 3878079 c.429C>T synonymous_variant 0.12
clpC1 4039427 p.Glu426Asp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267823 c.1014G>C synonymous_variant 0.17
aftB 4268601 p.Leu79Pro missense_variant 1.0
aftB 4269003 c.-167C>A upstream_gene_variant 0.12
ethR 4327660 p.Glu38Lys missense_variant 1.0
ethR 4327670 p.Pro41Leu missense_variant 0.17
ethR 4327709 p.Ala54Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408321 c.-119C>T upstream_gene_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0