TB-Profiler result

Run: ERR2229241
Summary

Run ID: ERR2229241

Sample name:

Date: 31-03-2023 16:52:56

Number of reads: 1122901

Percentage reads mapped: 99.05

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
ethA 4326292 c.1181delA frameshift_variant 0.15 ethionamide
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 5616 p.Ser126* stop_gained 0.17
gyrA 7362 p.Glu21Gln missense_variant 0.95
mshA 576008 p.Ala221Ser missense_variant 0.12
ccsA 620038 p.Pro50Ala missense_variant 0.14
ccsA 620192 p.Ala101Asp missense_variant 0.13
rpoB 762222 p.Thr806Ser missense_variant 0.15
rpoB 762454 p.His883Arg missense_variant 0.12
rpoC 766550 p.Phe1061Leu missense_variant 0.14
rpoC 767022 p.Asp1218Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777155 c.1326G>T synonymous_variant 0.12
mmpL5 778201 c.279dupC frameshift_variant 0.12
mmpS5 778661 p.Asp82Val missense_variant 0.14
mmpR5 779111 p.Gly41Val missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303840 p.Ala304Thr missense_variant 0.18
fbiC 1304464 p.Gly512Ser missense_variant 0.18
fbiC 1304679 p.Glu583Asp missense_variant 0.1
fbiC 1304680 p.Val584Leu missense_variant 0.1
embR 1416920 p.Arg143Lys missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474379 n.722G>C non_coding_transcript_exon_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
fabG1 1673413 c.-27G>T upstream_gene_variant 0.11
inhA 1674534 c.333G>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155234 p.Leu293Gln missense_variant 0.13
PPE35 2167955 c.2658A>C synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.51
PPE35 2170053 p.Thr187Ser missense_variant 0.51
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223364 c.-200G>T upstream_gene_variant 0.12
kasA 2519006 p.Ala298Ser missense_variant 0.13
ahpC 2725989 c.-204A>G upstream_gene_variant 0.11
fprA 3474457 p.Val151Leu missense_variant 0.17
fbiB 3641744 c.210A>G synonymous_variant 0.1
fbiB 3642140 c.606C>T synonymous_variant 0.12
alr 3840260 c.1161C>T synonymous_variant 0.2
alr 3840964 p.Thr153Ser missense_variant 0.14
clpC1 4039691 c.1014G>C synonymous_variant 0.11
embC 4242331 p.Glu823Asp missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.53
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4246699 c.186G>A synonymous_variant 0.15
embB 4247310 p.Arg266His missense_variant 0.12
aftB 4268619 p.Val73Gly missense_variant 0.4
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338486 c.36C>T synonymous_variant 0.13
whiB6 4338517 p.Arg2Gln missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0