TB-Profiler result

Run: SRR13180311

Summary

Run ID: SRR13180311

Sample name:

Date: 03-04-2023 08:17:51

Number of reads: 729025

Percentage reads mapped: 93.62

Strain: lineage4.3.4.2.1

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
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.99
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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490941 c.159C>T synonymous_variant 0.11
mshA 575224 c.-123delT upstream_gene_variant 0.12
mshA 575264 c.-84C>G upstream_gene_variant 0.18
mshA 575500 c.153G>T synonymous_variant 0.15
mshA 575617 c.270C>T synonymous_variant 0.13
mshA 575775 p.His143Arg missense_variant 0.15
mshA 576114 p.Arg256Leu missense_variant 0.18
ccsA 620441 p.Gly184Val missense_variant 0.11
ccsA 620641 p.Ala251Ser missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304361 c.1431C>A synonymous_variant 0.12
Rv1258c 1406696 c.645G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674389 p.Leu63Arg missense_variant 0.1
inhA 1674393 p.Asp64Glu missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155630 p.Trp161Leu missense_variant 0.12
katG 2155745 p.Gly123Arg missense_variant 0.1
katG 2155815 c.297G>T synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746318 c.1281C>A synonymous_variant 0.12
folC 2746825 c.774G>T synonymous_variant 0.14
pepQ 2859752 p.Gly223Ser missense_variant 0.17
pepQ 2860017 c.402T>C synonymous_variant 1.0
pepQ 2860616 c.-198G>A upstream_gene_variant 0.17
ribD 2987550 p.Met238Leu missense_variant 0.15
Rv2752c 3066162 c.30C>A synonymous_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339131 p.Pro5Leu missense_variant 0.12
fbiD 3339143 c.28_35delATCGGCTT frameshift_variant 0.14
fbiD 3339156 c.40_41insAGCCGATA frameshift_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612762 p.Leu119Ile missense_variant 0.14
fbiA 3640999 p.His153Asn missense_variant 0.12
fbiB 3641978 c.444C>A synonymous_variant 0.2
fbiB 3642301 p.Ala256Asp missense_variant 0.18
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039079 c.1626C>A synonymous_variant 0.14
clpC1 4039471 p.Ile412Val missense_variant 0.13
panD 4044462 c.-181T>C upstream_gene_variant 0.11
embC 4239783 c.-80C>A upstream_gene_variant 0.15
embC 4239978 p.Leu39Pro missense_variant 0.15
embC 4239992 p.Ala44Ser missense_variant 0.13
embC 4240566 c.706dupC frameshift_variant 0.13
embC 4241294 p.Ala478Ser missense_variant 0.12
embC 4241773 c.1911C>T synonymous_variant 0.17
embC 4242443 p.Pro861Thr missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243073 p.Gln1071Lys missense_variant 0.25
embA 4243241 c.9C>T synonymous_variant 0.22
embA 4243293 p.Gly21* stop_gained 0.2
embA 4243631 c.399G>T synonymous_variant 0.15
embA 4244497 c.1266delA frameshift_variant 0.13
embA 4245150 p.Val640Phe missense_variant 0.12
embA 4246290 p.Leu1020Ile missense_variant 0.11
embB 4246547 p.Pro12Thr missense_variant 0.12
embB 4247138 c.627dupG frameshift_variant 0.13
embB 4247247 p.Arg245Leu missense_variant 0.29
aftB 4268711 c.126G>A synonymous_variant 0.14
ethR 4327063 c.-486G>A upstream_gene_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0