TB-Profiler result

Run: ERR2229658
Summary

Run ID: ERR2229658

Sample name:

Date: 31-03-2023 17:23:56

Number of reads: 896900

Percentage reads mapped: 99.31

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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 0.95
mshA 575325 c.-23G>A upstream_gene_variant 0.11
ccsA 619899 c.9G>A synonymous_variant 0.18
rpoB 762220 p.Glu805Gly missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.13
mmpL5 776021 c.2460G>C synonymous_variant 0.12
mmpL5 776218 p.Ala755Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781642 p.Pro28Leu missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.4
rrl 1475816 n.2159C>A non_coding_transcript_exon_variant 0.13
rrl 1476362 n.2705C>G non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154143 p.Phe657Leu missense_variant 0.14
PPE35 2167745 p.Thr956Arg missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168993 c.1620A>T synonymous_variant 0.18
PPE35 2169602 c.1011C>A synonymous_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.46
Rv1979c 2222254 p.Ile304Asn missense_variant 0.12
Rv1979c 2222752 p.Thr138Met missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859493 p.Gly309Val missense_variant 0.13
Rv2752c 3065073 c.1119C>T synonymous_variant 0.14
Rv2752c 3065651 p.Arg181Cys missense_variant 0.14
ald 3087048 p.Pro77Ser missense_variant 0.12
Rv3236c 3612838 c.279G>A synonymous_variant 0.13
embC 4240008 p.Leu49Pro missense_variant 0.11
embC 4240947 p.Glu362Gly missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244087 c.855G>A synonymous_variant 0.13
embA 4244126 c.894C>T synonymous_variant 0.14
embA 4245745 p.Pro838Gln missense_variant 0.17
embA 4245832 p.Pro867Gln missense_variant 0.12
embA 4246050 p.Arg940Gly missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.15
embB 4247028 p.Leu172Arg missense_variant 0.21
aftB 4267197 p.Tyr547Phe missense_variant 0.18
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408255 c.-53A>G upstream_gene_variant 0.1
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0