TB-Profiler result

Run: SRR6832410
Summary

Run ID: SRR6832410

Sample name:

Date: 04-04-2023 17:24:27

Number of reads: 710824

Percentage reads mapped: 99.67

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 None 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8154 p.Thr285Ser missense_variant 0.22
gyrA 8253 p.Ile318Phe missense_variant 0.29
gyrA 8666 c.1365G>A synonymous_variant 0.25
ccsA 619831 c.-60T>G upstream_gene_variant 0.22
ccsA 619940 p.Ala17Val missense_variant 0.11
ccsA 620456 p.Ala189Val missense_variant 0.18
rpoC 765841 c.2472G>A synonymous_variant 0.22
rpoC 765868 c.2499G>A synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776386 p.Pro699Ser missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303391 c.463dupT frameshift_variant 0.33
Rv1258c 1406932 p.Trp137Gly missense_variant 0.25
embR 1416440 c.902_907delACCCAC disruptive_inframe_deletion 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
rrl 1476763 n.3106G>A non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168563 p.Pro684Thr missense_variant 0.25
PPE35 2169221 c.1392T>C synonymous_variant 0.33
PPE35 2170675 c.-63G>C upstream_gene_variant 1.0
Rv1979c 2223198 c.-34G>C upstream_gene_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289011 c.231C>G synonymous_variant 0.18
kasA 2518098 c.-17C>T upstream_gene_variant 0.15
pepQ 2860378 p.Ile14Thr missense_variant 0.13
ribD 2987040 c.202C>A synonymous_variant 0.29
ribD 2987073 p.Asp79Asn missense_variant 0.22
ald 3087380 c.561C>T synonymous_variant 1.0
Rv3083 3449901 c.1398C>T synonymous_variant 0.11
fprA 3474666 c.660G>A synonymous_variant 0.15
Rv3236c 3612602 p.Leu172Arg missense_variant 0.33
fbiB 3641921 c.387C>T synonymous_variant 0.17
fbiB 3641966 c.432C>T synonymous_variant 0.2
alr 3840227 c.1194C>T synonymous_variant 0.14
clpC1 4039997 c.708C>T synonymous_variant 0.2
clpC1 4040689 p.Thr6Ser missense_variant 0.13
clpC1 4040812 c.-108C>T upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243906 p.Asp225Val missense_variant 0.4
embA 4244957 c.1725C>T synonymous_variant 0.18
embB 4246547 p.Pro12Ser missense_variant 0.29
embB 4249732 c.3219C>G synonymous_variant 1.0
aftB 4267791 p.Pro349Arg missense_variant 0.33
ethA 4326523 c.951T>C synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408099 p.Leu35Pro missense_variant 1.0
gid 4408262 c.-60A>C upstream_gene_variant 1.0