TB-Profiler result

Run: SRR2101728
Summary

Run ID: SRR2101728

Sample name:

Date: 03-04-2023 23:52:57

Number of reads: 493806

Percentage reads mapped: 99.18

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 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
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
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrB 7237 p.Asn666Lys missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778147 p.Met112Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302807 c.-124G>T upstream_gene_variant 0.12
embR 1416714 p.Ile212Val missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472054 n.209G>A non_coding_transcript_exon_variant 0.11
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473792 n.135C>A non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102145 p.Ala300Thr missense_variant 0.11
PPE35 2168467 p.Leu716Ile missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288895 c.338_346delGCACGCCAC disruptive_inframe_deletion 0.4
pncA 2289466 c.-225T>A upstream_gene_variant 0.12
pncA 2290214 c.-973T>C upstream_gene_variant 0.2
folC 2746819 c.780T>C synonymous_variant 0.15
folC 2747202 c.397C>T synonymous_variant 0.11
pepQ 2860197 c.222T>C synonymous_variant 0.15
ribD 2987498 c.660C>A synonymous_variant 0.12
thyX 3067964 c.-19C>A upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087741 p.Thr308Ala missense_variant 0.15
fbiD 3338968 c.-150A>G upstream_gene_variant 0.17
fbiD 3339256 c.139T>C synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640406 c.-137G>T upstream_gene_variant 0.11
fbiA 3640654 p.Asp38Tyr missense_variant 0.18
fbiB 3641813 p.Leu93Phe missense_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240448 p.Gln196Lys missense_variant 0.1
embC 4240543 c.681G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243223 c.-10A>G upstream_gene_variant 0.2
embA 4245080 p.Trp616* stop_gained 0.11
embA 4245482 c.2250G>A synonymous_variant 0.15
embB 4248825 p.Ser771* stop_gained 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408165 p.Gly13Val missense_variant 0.14
gid 4408315 c.-113C>T upstream_gene_variant 0.11