TB-Profiler result

Run: SRR1166317

Summary

Run ID: SRR1166317

Sample name:

Date: 03-04-2023 01:24:58

Number of reads: 278637

Percentage reads mapped: 99.29

Strain: lineage4

Drug-resistance: HR-TB


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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
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
gyrB 6734 p.Asn499Asp missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781822 p.Lys88Met missense_variant 1.0 streptomycin
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779453 p.Gly155Glu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801154 p.Gly116Ser missense_variant 0.33
fbiC 1302987 c.57C>T synonymous_variant 0.17
fbiC 1304602 p.Cys558Arg missense_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674496 p.Pro99Ala missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101793 p.Trp417* stop_gained 0.67
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289714 c.-473G>A upstream_gene_variant 0.4
ahpC 2726153 c.-40G>A upstream_gene_variant 0.33
folC 2746181 p.Val473Asp missense_variant 0.4
Rv2752c 3064875 c.1317C>G synonymous_variant 1.0
Rv2752c 3065294 p.Val300Phe missense_variant 0.4
ald 3086787 c.-33A>G upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
fbiA 3640984 p.Asp148Asn missense_variant 0.33
fbiA 3641477 p.Asp312Gly missense_variant 1.0
clpC1 4038442 p.Ala755Thr missense_variant 0.2
embC 4242641 p.Arg927Cys missense_variant 0.2
embA 4243078 c.-155C>T upstream_gene_variant 0.15
ethA 4326533 p.Thr314Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1440del transcript_ablation 1.0