TB-Profiler result

Run: SRR4033767

Summary

Run ID: SRR4033767

Sample name:

Date: 04-04-2023 06:19:08

Number of reads: 1002629

Percentage reads mapped: 99.63

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 0.99
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8327 c.1026C>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491200 p.Arg140Gly missense_variant 0.2
rpoB 761852 c.2046C>A synonymous_variant 0.12
rpoC 763916 p.Glu183* stop_gained 0.12
rpoC 764534 c.1167delG frameshift_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775665 p.Trp939Leu missense_variant 0.14
mmpL5 777569 c.912C>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475287 n.1630G>T non_coding_transcript_exon_variant 0.17
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.33
rrl 1475454 n.1797G>A non_coding_transcript_exon_variant 0.22
rrl 1475964 n.2307G>A non_coding_transcript_exon_variant 0.12
rpsA 1834853 p.Ala438Thr missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155070 p.Ala348Ser missense_variant 0.11
PPE35 2167680 p.Ser978* stop_gained 0.13
PPE35 2168139 p.Ala825Val missense_variant 0.11
PPE35 2169320 p.Leu431Phe missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519061 p.Pro316His missense_variant 0.18
pepQ 2859905 p.Val172Leu missense_variant 0.11
Rv2752c 3064552 p.Arg547Pro missense_variant 0.15
Rv2752c 3065823 c.368delC frameshift_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073881 c.591C>T synonymous_variant 0.25
thyA 3074035 p.Cys146Phe missense_variant 0.11
thyA 3074069 p.Val135Phe missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449327 p.Arg275His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613150 c.-34G>T upstream_gene_variant 0.12
rpoA 3878042 p.Gly156Cys missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267787 c.1050G>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407553 p.Arg217Gln missense_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0