TB-Profiler result

Run: ERR2229227

Summary

Run ID: ERR2229227

Sample name:

Date: 31-03-2023 16:50:46

Number of reads: 1091829

Percentage reads mapped: 99.15

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
gyrB 6606 p.Tyr456Cys missense_variant 0.12
gyrA 6736 c.-566C>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491129 p.Thr116Asn missense_variant 0.11
rpoB 760955 c.1149C>A synonymous_variant 0.12
rpoC 767016 p.Ala1216Asp missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776414 c.2067C>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416887 p.Arg154Leu missense_variant 0.14
embR 1416909 p.Gly147Trp missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473843 n.186G>C non_coding_transcript_exon_variant 0.4
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
rpsA 1833765 p.Asp75Gly missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 c.2868C>G synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169302 p.Met437Phe missense_variant 0.15
PPE35 2169476 p.Thr379Ser missense_variant 0.12
PPE35 2169602 c.1011C>A synonymous_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.11
PPE35 2169749 c.864A>C synonymous_variant 0.11
PPE35 2169890 c.723C>T synonymous_variant 0.15
PPE35 2169893 c.720C>A synonymous_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.3
PPE35 2170053 p.Thr187Ser missense_variant 0.3
PPE35 2170147 p.Ser156Ala missense_variant 0.15
PPE35 2170528 p.Ser29Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714144 p.Gln397* stop_gained 0.17
eis 2714382 c.951T>C synonymous_variant 0.13
pepQ 2859744 c.675G>T synonymous_variant 0.11
ribD 2987210 c.372T>C synonymous_variant 0.14
Rv2752c 3064526 p.Ile556Phe missense_variant 0.13
Rv2752c 3064833 c.1359C>T synonymous_variant 0.22
Rv2752c 3065227 p.Glu322Gly missense_variant 0.11
Rv2752c 3065321 p.Ala291Ser missense_variant 0.13
Rv2752c 3067144 c.-953G>C upstream_gene_variant 0.14
thyX 3067470 p.Asn159Thr missense_variant 0.18
thyX 3067694 c.252G>T synonymous_variant 0.2
whiB7 3568522 p.Leu53* stop_gained 0.12
Rv3236c 3612492 p.Leu209Val missense_variant 0.25
fbiA 3640363 c.-180C>T upstream_gene_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.14
embC 4241191 c.1329C>A synonymous_variant 0.17
embC 4241631 p.Phe590Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245305 c.2073G>C synonymous_variant 0.2
embA 4245855 p.Gly875Ser missense_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
aftB 4268025 p.Val271Ala missense_variant 0.14
ethR 4326814 c.-735G>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0