TB-Profiler result

Run: ERR11465351
Summary

Run ID: ERR11465351

Sample name:

Date: 03-01-2024 02:54:41

Number of reads: 3316052

Percentage reads mapped: 99.18

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.95
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8813 p.Asp504Glu missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.97
mshA 575679 p.Asn111Ser missense_variant 0.98
mshA 575893 c.546C>G synonymous_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760406 c.600G>C synonymous_variant 0.12
rpoB 760424 c.618C>G synonymous_variant 0.12
rpoB 760611 c.805_807delTTGinsCTC synonymous_variant 0.17
rpoB 761892 p.Ile696Val missense_variant 0.11
rpoB 761930 c.2124G>C synonymous_variant 0.14
rpoB 762083 c.2277T>C synonymous_variant 0.12
rpoB 762086 c.2280G>C synonymous_variant 0.13
rpoB 762131 c.2325C>G synonymous_variant 0.12
rpoC 763028 c.-342T>C upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.13
rpoC 763040 c.-330C>G upstream_gene_variant 0.12
rpoC 763103 c.-267G>C upstream_gene_variant 0.13
rpoC 763115 c.-255T>C upstream_gene_variant 0.13
rpoC 763546 c.177A>G synonymous_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765499 c.2130C>G synonymous_variant 0.2
rpoC 766345 c.2976T>C synonymous_variant 0.12
rpoC 766348 c.2979A>G synonymous_variant 0.12
rpoC 766369 c.3000C>G synonymous_variant 0.15
rpoC 766381 c.3012C>T synonymous_variant 0.18
rpoC 766384 c.3015A>G synonymous_variant 0.18
rpoC 766393 c.3024C>G synonymous_variant 0.15
rpoC 766426 c.3057C>T synonymous_variant 0.18
rpoC 766429 c.3060C>G synonymous_variant 0.19
rpoC 766447 c.3078T>C synonymous_variant 0.17
rpoC 766459 c.3090G>C synonymous_variant 0.13
rpoC 766516 c.3147C>G synonymous_variant 0.13
rpoC 766517 p.Thr1050Ser missense_variant 0.13
rpoC 766528 c.3159T>G synonymous_variant 0.12
rpoC 766540 p.Asp1057Glu missense_variant 0.11
rpoC 766543 c.3174C>T synonymous_variant 0.13
rpoC 766549 c.3180G>C synonymous_variant 0.12
rpoC 766774 c.3405T>C synonymous_variant 0.17
rpoC 766837 c.3468G>C synonymous_variant 0.15
rpoC 766843 c.3474T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781733 c.174G>C synonymous_variant 0.12
rpsL 781736 c.177T>C synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.16
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.17
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.16
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.17
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.2
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.2
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.23
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.15
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.15
rrl 1475989 n.2332T>A non_coding_transcript_exon_variant 0.14
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.15
rrl 1476088 n.2431A>T non_coding_transcript_exon_variant 0.16
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.16
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.14
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.15
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.15
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.15
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.16
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.16
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.16
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.19
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.16
inhA 1674486 c.285T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518783 c.669T>C synonymous_variant 0.15
kasA 2518795 c.681C>G synonymous_variant 0.14
kasA 2518811 p.Asp233Asn missense_variant 0.13
kasA 2518816 c.702C>T synonymous_variant 0.13
kasA 2518825 c.711T>C synonymous_variant 0.13
kasA 2518843 c.729T>C synonymous_variant 0.14
kasA 2518847 p.Leu245Met missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038596 c.2109A>G synonymous_variant 0.13
clpC1 4039898 c.807C>G synonymous_variant 0.14
embC 4241104 c.1242G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.57
whiB6 4338595 c.-75delG upstream_gene_variant 1.0