TB-Profiler result

Run: ERR2229387
Summary

Run ID: ERR2229387

Sample name:

Date: 31-03-2023 17:08:52

Number of reads: 806519

Percentage reads mapped: 99.14

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 7281 c.-21T>C upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8938 p.Gly546Val missense_variant 0.14
fgd1 491357 p.Phe192Tyr missense_variant 0.29
mshA 575576 p.Leu77Met missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.31
mshA 576114 p.Arg256Pro missense_variant 0.18
rpoB 759611 c.-195delC upstream_gene_variant 0.22
rpoB 760137 p.Ala111Ser missense_variant 0.18
rpoB 761236 p.Met477Lys missense_variant 0.18
rpoB 761247 c.1444delA frameshift_variant 0.2
rpoC 763785 p.Val139Asp missense_variant 0.13
rpoC 765148 c.1779C>A synonymous_variant 0.17
rpoC 766225 c.2856G>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778183 p.Pro100Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303429 p.Tyr167His missense_variant 0.12
fbiC 1303507 p.Pro193Thr missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305265 p.Gly779Cys missense_variant 0.2
embR 1417248 c.99delC frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474527 n.870T>A non_coding_transcript_exon_variant 0.13
rrl 1475789 n.2132C>A non_coding_transcript_exon_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
inhA 1674911 p.Pro237Leu missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102389 c.654G>C synonymous_variant 0.14
ndh 2102392 c.651C>A synonymous_variant 0.14
PPE35 2167805 p.Tyr936* stop_gained 0.13
PPE35 2167814 c.2799C>T synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.24
PPE35 2169902 p.Leu237Phe missense_variant 0.26
PPE35 2169910 p.Asn235Tyr missense_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2222227 p.Phe313Tyr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289875 c.-634C>A upstream_gene_variant 0.17
kasA 2519128 c.1014G>C synonymous_variant 0.19
kasA 2519131 c.1017G>C synonymous_variant 0.19
kasA 2519140 c.1026G>C synonymous_variant 0.18
kasA 2519143 c.1029G>C synonymous_variant 0.18
folC 2746773 p.Val276Leu missense_variant 0.17
pepQ 2860308 p.Ser37Arg missense_variant 0.13
Rv2752c 3064693 p.Asp500Gly missense_variant 0.25
thyX 3067340 c.606G>A synonymous_variant 0.14
thyX 3067754 c.192C>A synonymous_variant 0.12
thyX 3068024 c.-79A>G upstream_gene_variant 0.2
thyA 3073769 c.703C>A synonymous_variant 0.19
fprA 3474568 p.Pro188Thr missense_variant 0.14
whiB7 3568572 c.108C>T synonymous_variant 0.14
clpC1 4038699 p.Gly669Ala missense_variant 0.12
clpC1 4039654 p.Thr351Ser missense_variant 0.2
clpC1 4039674 p.Pro344Gln missense_variant 0.14
clpC1 4039676 c.1029G>A synonymous_variant 0.13
clpC1 4039682 c.1023C>T synonymous_variant 0.13
clpC1 4039691 c.1014G>C synonymous_variant 0.18
clpC1 4039730 c.975C>G synonymous_variant 0.17
clpC1 4039912 p.Phe265Leu missense_variant 0.2
clpC1 4040044 p.Gly221Cys missense_variant 0.15
clpC1 4040235 p.Gly157Val missense_variant 0.12
embC 4239861 c.-2T>A upstream_gene_variant 0.12
embC 4242171 p.Thr770Ile missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246726 c.213G>T synonymous_variant 0.17
aftB 4268051 c.786G>A synonymous_variant 0.14
aftB 4268536 p.Gly101Trp missense_variant 0.22
ethA 4326945 p.Asn177Tyr missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0