TB-Profiler result

Run: SRR11033681
Summary

Run ID: SRR11033681

Sample name:

Date: 02-04-2023 20:18:25

Number of reads: 28556054

Percentage reads mapped: 99.55

Strain: lineage4.8;lineage4.3.3

Drug-resistance: Other

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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 0.16
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.86
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.15
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
rpsL 781687 p.Lys43Arg missense_variant 0.16 streptomycin
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 0.21
gyrA 8040 p.Gly247Ser missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.15
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 0.78
rrl 1475593 n.1941dupG non_coding_transcript_exon_variant 0.15
rpsA 1834836 p.Met432Thr missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.17
PPE35 2168149 p.Pro822Ser missense_variant 0.77
PPE35 2168343 p.Gly757Val missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.16
ahpC 2726066 c.-127G>A upstream_gene_variant 0.88
folC 2746340 p.Ala420Val missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.16
clpC1 4038287 c.2418C>T synonymous_variant 0.16
clpC1 4038968 c.1737G>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244728 p.Phe499Cys missense_variant 0.88
embA 4245131 c.1899G>A synonymous_variant 0.84
embB 4247395 c.882C>T synonymous_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.19