TB-Profiler result

Run: SRR6856096
Summary

Run ID: SRR6856096

Sample name:

Date: 04-04-2023 17:55:54

Number of reads: 565908

Percentage reads mapped: 98.87

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 6477 p.Ser413Trp missense_variant 0.11
gyrB 6720 p.Asp494Gly missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575739 p.Ala131Gly missense_variant 0.12
mshA 576240 p.Ala298Val missense_variant 0.11
ccsA 620750 p.Trp287* stop_gained 0.1
ccsA 620776 p.Asn296Asp missense_variant 0.1
rpoC 762962 c.-408C>A upstream_gene_variant 0.1
rpoC 766085 p.Pro906Ala missense_variant 1.0
rpoC 766486 c.3117A>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777126 c.1354delA frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304079 c.1149A>G synonymous_variant 0.13
atpE 1460992 c.-53A>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472185 n.340C>T non_coding_transcript_exon_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.1
rpsA 1833545 p.Pro2Ser missense_variant 0.11
rpsA 1834647 p.Tyr369Cys missense_variant 1.0
tlyA 1917823 c.-117C>G upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101672 c.1368_1370delGGC disruptive_inframe_deletion 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518272 p.Lys53Arg missense_variant 0.11
Rv3236c 3612195 c.921delC frameshift_variant 0.12
alr 3840764 c.657G>C synonymous_variant 1.0
embC 4241761 c.1899G>T synonymous_variant 0.15
embC 4241865 c.2004delG frameshift_variant 0.14
embC 4242070 c.2208T>C synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243813 p.Arg194Gln missense_variant 1.0
embA 4244841 p.Arg537Trp missense_variant 0.15
embA 4245847 p.Ser872Cys missense_variant 0.15
ethR 4327135 c.-414T>C upstream_gene_variant 0.11
whiB6 4338398 p.Thr42Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0