TB-Profiler result

Run: ERR2229441
Summary

Run ID: ERR2229441

Sample name:

Date: 31-03-2023 17:12:04

Number of reads: 1022659

Percentage reads mapped: 99.35

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 0.23
mshA 576375 p.Ala343Val missense_variant 0.11
ccsA 619862 c.-29G>T upstream_gene_variant 0.12
rpoB 760412 c.606C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.17
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304461 p.Asp511Asn missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473994 n.337C>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474101 n.444C>T non_coding_transcript_exon_variant 0.13
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
fabG1 1673683 p.Val82Phe missense_variant 0.14
inhA 1674536 p.Pro112His missense_variant 0.2
inhA 1674782 c.583dupC frameshift_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.19
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169308 c.1305C>T synonymous_variant 0.16
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519011 c.897G>A synonymous_variant 0.13
eis 2714950 c.382delC frameshift_variant 0.12
eis 2715465 c.-133G>T upstream_gene_variant 0.15
folC 2747085 p.Val172Met missense_variant 0.13
pepQ 2860154 p.Glu89Gln missense_variant 0.13
pepQ 2860615 c.-197T>C upstream_gene_variant 0.12
Rv2752c 3064822 p.Val457Ala missense_variant 0.13
Rv2752c 3064825 p.Asp456Val missense_variant 0.14
Rv2752c 3064828 p.Gly455Asp missense_variant 0.14
thyA 3074099 p.Ser125Thr missense_variant 0.15
ald 3087891 p.Asp358Asn missense_variant 0.14
fprA 3473982 c.-25C>T upstream_gene_variant 0.13
fbiB 3642683 c.1149C>T synonymous_variant 0.15
alr 3840427 p.Gly332Ser missense_variant 0.13
rpoA 3877573 p.Pro312Leu missense_variant 0.12
clpC1 4039018 p.Ser563Ala missense_variant 0.11
clpC1 4039022 c.1683A>G synonymous_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243377 p.Ser49Cys missense_variant 0.17
embB 4246536 p.Arg8His missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.57
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4246584 p.Arg24Pro missense_variant 0.67
embB 4248702 c.2192delC frameshift_variant 0.12
aftB 4267991 c.845delC frameshift_variant 0.17
ethA 4326900 p.Pro192Thr missense_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407686 p.Glu173Lys missense_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0