TB-Profiler result

Run: SRR4037880
Summary

Run ID: SRR4037880

Sample name:

Date: 04-04-2023 07:44:24

Number of reads: 696448

Percentage reads mapped: 99.6

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 5829 p.Met197Thr missense_variant 0.12
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7700 c.399G>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764197 c.828G>A synonymous_variant 0.13
rpoC 764592 c.1224delC frameshift_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775915 p.Ala856Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406408 c.933G>A synonymous_variant 0.17
Rv1258c 1406446 p.Gly299Cys missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471975 n.130G>C non_coding_transcript_exon_variant 0.12
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
inhA 1674123 c.-79T>C upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102268 p.Val259Ile missense_variant 0.33
PPE35 2169044 c.1569G>A synonymous_variant 0.12
Rv1979c 2223261 c.-97A>G upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518492 p.Tyr126* stop_gained 0.12
ribD 2987570 c.732C>A synonymous_variant 0.29
Rv2752c 3064860 c.1332G>A synonymous_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 0.89
thyA 3074386 p.Leu29Gln missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474515 p.Pro170Leu missense_variant 0.17
Rv3236c 3612318 p.Arg267Gly missense_variant 0.14
fbiB 3641778 p.Ala82Thr missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039132 p.Val525Ile missense_variant 0.18
clpC1 4040226 p.Gly160Glu missense_variant 0.33
panD 4044000 c.282C>T synonymous_variant 0.2
embC 4241294 p.Ala478Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243747 p.Gly172Val missense_variant 0.11
embA 4246008 p.Arg926Trp missense_variant 0.18
embB 4249678 c.3165C>T synonymous_variant 0.2
aftB 4268276 c.561G>A synonymous_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0