TB-Profiler result

Run: SRR23402847
Summary

Run ID: SRR23402847

Sample name:

Date: 15-03-2023 14:42:58

Number of reads: 18157735

Percentage reads mapped: 99.65

Strain: lineage4.8;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
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 0.45
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.51
lineage4.1.2 Euro-American T;H None 0.46
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.45
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 0.51
gyrA 9304 p.Gly668Asp missense_variant 0.47
fgd1 491591 p.Lys270Met missense_variant 0.46
mshA 575679 p.Asn111Ser missense_variant 0.44
rpoB 760115 c.309C>T synonymous_variant 0.43
rpoB 760838 c.1032G>A synonymous_variant 0.51
rpoC 764861 p.Leu498Val missense_variant 0.57
rpoC 765150 p.Gly594Glu missense_variant 0.45
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.52
rpsA 1834770 p.Gln410Arg missense_variant 0.56
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917999 c.60T>C synonymous_variant 0.47
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290014 c.-773T>C upstream_gene_variant 0.56
kasA 2518076 c.-39C>T upstream_gene_variant 0.51
eis 2715491 c.-159G>T upstream_gene_variant 0.59
thyA 3073677 c.790_791insGAG conservative_inframe_insertion&splice_region_variant 0.49
ald 3086788 c.-32T>C upstream_gene_variant 0.49
fprA 3473996 c.-10_-9insA upstream_gene_variant 0.39
fprA 3475012 p.Asp336Asn missense_variant 0.52
alr 3841546 c.-126C>A upstream_gene_variant 0.56
alr 3841612 c.-193_-192insC upstream_gene_variant 0.52
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.48
aftB 4269087 c.-251G>A upstream_gene_variant 0.52
ethA 4326395 p.Gln360Arg missense_variant 0.53
ethA 4326582 p.Asn298His missense_variant 0.61
whiB6 4338595 c.-75delG upstream_gene_variant 1.0