TB-Profiler result

Run: ERR2229154
Summary

Run ID: ERR2229154

Sample name:

Date: 31-03-2023 16:45:17

Number of reads: 604092

Percentage reads mapped: 99.53

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 1.0
fgd1 490721 c.-62C>A upstream_gene_variant 0.12
mshA 575502 p.Val52Ala missense_variant 0.33
ccsA 620730 p.His280Gln missense_variant 0.29
rpoB 761473 p.Arg556His missense_variant 0.14
rpoC 763762 p.Phe131Leu missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778623 c.282delC frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
atpE 1461219 c.175T>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474751 n.1094G>T non_coding_transcript_exon_variant 0.4
rrl 1475960 n.2303C>A non_coding_transcript_exon_variant 0.15
rpsA 1833724 c.183C>A synonymous_variant 0.17
rpsA 1833987 p.Pro149His missense_variant 0.33
rpsA 1834231 c.690T>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102343 p.Ala234Ser missense_variant 0.29
ndh 2102485 c.558C>T synonymous_variant 0.2
ndh 2102799 p.Val82Phe missense_variant 0.25
ndh 2102875 c.168C>T synonymous_variant 0.18
ndh 2103012 p.Pro11Thr missense_variant 0.17
katG 2154065 p.Gly683Ser missense_variant 0.14
katG 2154463 p.Ala550Val missense_variant 0.12
katG 2154975 c.1137C>T synonymous_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.39
PPE35 2167967 c.2646A>C synonymous_variant 0.39
PPE35 2167975 p.Ala880Thr missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.68
PPE35 2170053 p.Thr187Ser missense_variant 0.69
Rv1979c 2222333 p.Gly278Arg missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289381 c.-140C>A upstream_gene_variant 0.13
folC 2747482 c.117G>T synonymous_variant 0.17
pepQ 2859469 p.Leu317Pro missense_variant 0.12
pepQ 2860526 c.-108C>A upstream_gene_variant 0.13
Rv2752c 3064551 c.1641C>A synonymous_variant 0.13
Rv2752c 3064772 p.Ala474Thr missense_variant 0.13
thyX 3068001 c.-56G>T upstream_gene_variant 0.17
thyX 3068143 c.-198G>T upstream_gene_variant 0.12
fprA 3474143 p.Trp46Tyr missense_variant 0.22
fprA 3474165 c.159C>G synonymous_variant 0.29
Rv3236c 3612177 c.940C>A synonymous_variant 0.15
rpoA 3878491 p.Arg6His missense_variant 0.2
clpC1 4038997 c.1708T>C synonymous_variant 0.15
clpC1 4039003 p.Asn568Asp missense_variant 0.14
embC 4241106 p.Arg415Leu missense_variant 0.18
embC 4241848 c.1986C>T synonymous_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4247028 p.Leu172Gln missense_variant 0.5
aftB 4267988 c.849G>A synonymous_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0