TB-Profiler result

Run: SRR4114390

Summary

Run ID: SRR4114390

Sample name:

Date: 04-04-2023 07:50:13

Number of reads: 1729945

Percentage reads mapped: 99.88

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 5482 c.243C>A synonymous_variant 0.11
gyrA 6817 c.-485G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.94
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762644 c.-726T>C upstream_gene_variant 0.33
rpoC 763262 c.-108C>T upstream_gene_variant 0.12
rpoC 764846 p.Glu493Lys missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776257 p.Ala742Pro missense_variant 0.1
mmpL5 776489 c.1992T>C synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417053 p.Pro99Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
rpsA 1833944 p.Lys135Glu missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156374 c.-263A>T upstream_gene_variant 0.11
PPE35 2168264 c.2349G>T synonymous_variant 0.12
Rv1979c 2222538 c.627C>T synonymous_variant 0.12
Rv1979c 2222905 p.Gly87Val missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288757 p.Gly162Val missense_variant 0.2
kasA 2519107 c.993T>C synonymous_variant 0.12
Rv2752c 3065728 p.Ala155Val missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087418 p.Asn200Ser missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3640872 c.-663C>T upstream_gene_variant 1.0
fbiB 3642358 p.Leu275Arg missense_variant 0.5
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4242015 p.Phe718Ser missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.19
embB 4246556 p.Ala15Pro missense_variant 0.19
embB 4246563 p.Leu17Trp missense_variant 0.14
embB 4246786 p.Met91Ile missense_variant 0.11
embB 4249617 p.Gly1035Asp missense_variant 0.13
ubiA 4269189 p.Ser215Arg missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0