TB-Profiler result

Run: ERR163965
Summary

Run ID: ERR163965

Sample name:

Date: 21-10-2023 03:47:37

Number of reads: 2615082

Percentage reads mapped: 92.66

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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.98
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 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7760 c.459C>T synonymous_variant 0.13
gyrA 7763 c.462T>C synonymous_variant 0.13
gyrA 7799 c.498A>G synonymous_variant 0.16
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9311 c.2010C>T synonymous_variant 0.13
mshA 575537 p.Asp64Asn missense_variant 0.97
rpoB 760223 c.417T>C synonymous_variant 0.12
rpoC 763594 c.225C>T synonymous_variant 0.12
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
rpsL 781832 c.273T>C synonymous_variant 0.13
rpsL 781841 c.282C>G synonymous_variant 0.12
rplC 800648 c.-161A>C upstream_gene_variant 0.13
rplC 800654 c.-155T>C upstream_gene_variant 0.15
rplC 801174 c.366T>C synonymous_variant 0.14
rplC 801222 c.414T>C synonymous_variant 0.15
rplC 801228 c.420T>C synonymous_variant 0.14
rplC 801246 c.438C>G synonymous_variant 0.13
rplC 801249 c.441T>G synonymous_variant 0.13
rplC 801255 c.447C>T synonymous_variant 0.13
fbiC 1304034 c.1104A>G synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.16
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.17
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.21
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.21
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.28
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.89
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.24
rpsA 1834225 c.684C>G synonymous_variant 0.16
rpsA 1834297 c.756C>G synonymous_variant 0.16
rpsA 1834303 c.762T>G synonymous_variant 0.15
rpsA 1834306 c.765T>C synonymous_variant 0.16
rpsA 1834639 c.1098T>C synonymous_variant 0.12
rpsA 1834666 c.1125G>C synonymous_variant 0.13
rpsA 1834688 c.1147_1149delAGTinsTCC synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878028 c.480G>C synonymous_variant 0.12
rpoA 3878031 c.477T>C synonymous_variant 0.13
rpoA 3878040 c.468T>C synonymous_variant 0.14
rpoA 3878055 c.453A>G synonymous_variant 0.15
rpoA 3878061 c.447G>C synonymous_variant 0.13
rpoA 3878067 c.441C>G synonymous_variant 0.13
rpoA 3878070 c.438T>C synonymous_variant 0.13
rpoA 3878220 c.288C>T synonymous_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.95
clpC1 4039586 c.1119G>C synonymous_variant 0.16
clpC1 4039610 c.1095G>C synonymous_variant 0.21
clpC1 4039616 c.1089G>C synonymous_variant 0.21
clpC1 4039622 c.1083C>G synonymous_variant 0.19
panD 4043938 p.Ile115Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247389 c.876C>A synonymous_variant 0.11
embB 4248070 c.1557T>C synonymous_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0