TB-Profiler result

Run: SRR14782212
Summary

Run ID: SRR14782212

Sample name:

Date: 03-04-2023 11:16:45

Number of reads: 5129434

Percentage reads mapped: 99.66

Strain: lineage4.8;lineage4.2.1.1

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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 0.16
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.84
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.15
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.14
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
gid 4407713 c.489delA frameshift_variant 0.12 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 0.12
gyrA 9263 c.1962C>T synonymous_variant 0.89
mshA 576108 p.Ala254Gly missense_variant 0.26
mshA 576482 p.Val379Leu missense_variant 0.12
mshA 576574 c.1227T>C synonymous_variant 0.86
rpoC 766984 c.3615G>A synonymous_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.14
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 0.89
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.87
PPE35 2169879 p.Phe245Cys missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714278 p.Asp352Gly missense_variant 0.82
ald 3086742 c.-78A>C upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.15
rpoA 3877485 c.1023C>T synonymous_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.19