TB-Profiler result

Run: SRR8420475
Summary

Run ID: SRR8420475

Sample name:

Date: 04-04-2023 21:22:51

Number of reads: 936125

Percentage reads mapped: 98.35

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
katG 2155222 p.Gly297Val missense_variant 0.14 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575757 p.Leu137Pro missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304565 c.1638delT frameshift_variant 0.15
fbiC 1304613 c.1683T>C synonymous_variant 0.11
embR 1416902 p.Val149Ala missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472389 n.544G>C non_coding_transcript_exon_variant 0.1
rrl 1473483 n.-175C>A upstream_gene_variant 0.15
rrl 1474389 n.732G>T non_coding_transcript_exon_variant 0.13
rrl 1476472 n.2815A>G non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 0.96
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714184 c.1149T>G synonymous_variant 0.1
pepQ 2859574 p.Ala282Val missense_variant 0.12
thyX 3067425 p.Val174Glu missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448460 c.-43delA upstream_gene_variant 0.12
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474659 p.Leu218Pro missense_variant 0.12
whiB7 3568595 p.Phe29Leu missense_variant 0.1
Rv3236c 3612155 p.Arg321Leu missense_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiA 3641372 p.Gly277Ala missense_variant 0.2
fbiA 3641419 p.Gly293Ser missense_variant 0.12
rpoA 3877967 p.Thr181Ser missense_variant 0.15
clpC1 4039526 c.1179G>C synonymous_variant 0.11
clpC1 4039530 p.Asp392Ala missense_variant 0.11
embC 4241045 p.Gly395Ser missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245975 p.Asp915Tyr missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.24
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246563 p.Leu17Trp missense_variant 0.19
embB 4246567 c.54G>T synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338659 c.-138A>G upstream_gene_variant 0.11