TB-Profiler result

Run: ERR2229573
Summary

Run ID: ERR2229573

Sample name:

Date: 31-03-2023 17:19:40

Number of reads: 1076480

Percentage reads mapped: 98.92

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
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576313 c.966T>C synonymous_variant 0.14
ccsA 620520 c.630C>A synonymous_variant 0.22
ccsA 620650 p.Ala254Ser missense_variant 0.14
ccsA 620659 p.Arg257Cys missense_variant 0.13
rpoB 761317 p.Gly504Val missense_variant 0.12
rpoB 761845 p.Gln680Arg missense_variant 0.11
rpoB 762513 p.Asp903Asn missense_variant 0.14
rpoC 764141 p.Ala258Thr missense_variant 0.13
rpoC 764541 p.Val391Gly missense_variant 0.17
rpoC 764543 p.Thr392Asp missense_variant 0.18
rpoC 765194 p.Thr609Ala missense_variant 0.11
rpoC 765912 p.Glu848Val missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776009 c.2472A>G synonymous_variant 0.2
mmpL5 776018 c.2463G>C synonymous_variant 0.14
mmpL5 776021 c.2460G>C synonymous_variant 0.15
mmpL5 776290 p.Gly731Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303681 p.Leu251Met missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473822 n.165A>T non_coding_transcript_exon_variant 0.14
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475144 n.1487G>T non_coding_transcript_exon_variant 0.12
rrl 1476321 n.2664A>T non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
fabG1 1673786 p.Ala116Glu missense_variant 0.2
fabG1 1673815 p.Ser126Gly missense_variant 0.14
fabG1 1674089 p.Val217Gly missense_variant 0.22
rpsA 1834514 p.Glu325* stop_gained 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102505 p.Pro180Thr missense_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.24
PPE35 2167967 c.2646A>C synonymous_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.17
PPE35 2169725 c.888T>C synonymous_variant 0.16
PPE35 2169732 p.Asn294Ser missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289698 c.-458delT upstream_gene_variant 0.15
eis 2715040 p.Arg98Leu missense_variant 0.13
pepQ 2859743 p.Val226Phe missense_variant 0.12
Rv2752c 3065413 p.Ser260Leu missense_variant 0.13
thyA 3074570 c.-100delT upstream_gene_variant 0.12
thyA 3074580 c.-109T>C upstream_gene_variant 0.12
fbiD 3339677 p.Cys187Tyr missense_variant 0.15
alr 3840439 p.Val328Leu missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.23
clpC1 4038761 c.1944C>A synonymous_variant 0.13
clpC1 4040390 c.315C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244722 p.Gln497Arg missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.54
embB 4246555 c.42G>C synonymous_variant 0.58
embB 4246556 p.Ala15Pro missense_variant 0.58
embB 4247053 c.540C>T synonymous_variant 0.17
embB 4247059 c.546C>G synonymous_variant 0.17
embB 4247060 p.Pro183Ala missense_variant 0.17
embB 4247066 p.Ile185Val missense_variant 0.17
embB 4248706 c.2193G>A synonymous_variant 0.12
ethA 4326050 p.Asp475Gly missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0