TB-Profiler result

Run: SRR7755684
Summary

Run ID: SRR7755684

Sample name:

Date: 04-04-2023 20:15:12

Number of reads: 5827240

Percentage reads mapped: 99.38

Strain: lineage4.8;lineage4.2.1

Drug-resistance: HR-TB

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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
lineage4.2 Euro-American H;T;LAM None 0.44
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.57
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.41
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
katG 2155168 p.Ser315Thr missense_variant 0.36 isoniazid
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 0.46
gyrA 9304 p.Gly668Asp missense_variant 0.39
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 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.58
PPE35 2168247 p.Leu789Arg missense_variant 0.58
PPE35 2169879 p.Phe245Cys missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289952 c.-711C>G upstream_gene_variant 0.51
folC 2747536 c.63G>A synonymous_variant 0.37
ald 3086742 c.-78A>C upstream_gene_variant 0.43
ald 3086788 c.-32T>C upstream_gene_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.46
rpoA 3878641 c.-135_-134insG upstream_gene_variant 0.11
clpC1 4039729 p.Asp326Asn missense_variant 0.58
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 0.42
ethA 4328376 c.-903G>C upstream_gene_variant 0.47
whiB6 4338595 c.-75delG upstream_gene_variant 1.0