TB-Profiler result

Run: SRR4034671
Summary

Run ID: SRR4034671

Sample name:

Date: 04-04-2023 06:57:48

Number of reads: 804394

Percentage reads mapped: 99.51

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;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
katG 2154659 c.1452delT frameshift_variant 0.17 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
gyrB 5878 c.639G>A synonymous_variant 0.14
gyrB 6783 p.Asp515Gly missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8397 p.Val366Ile missense_variant 0.12
gyrA 8555 c.1254G>A synonymous_variant 0.11
gyrA 8963 c.1662C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575380 c.33G>A synonymous_variant 0.18
rpoB 759747 c.-60C>A upstream_gene_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 763353 c.-17_-16insG upstream_gene_variant 0.13
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775811 c.2669delT frameshift_variant 0.17
mmpL5 776319 p.Ser721Thr missense_variant 0.11
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781576 p.Gln6Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472116 n.273delA non_coding_transcript_exon_variant 0.15
rrs 1472290 n.445C>A non_coding_transcript_exon_variant 0.18
rrs 1472319 n.478_481delAGGT non_coding_transcript_exon_variant 0.12
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.11
rrl 1474781 n.1124C>A non_coding_transcript_exon_variant 0.12
rrl 1476040 n.2383C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154072 c.2040C>G synonymous_variant 0.12
katG 2154488 p.Asp542Asn missense_variant 0.14
PPE35 2167692 p.Gly974Val missense_variant 0.2
PPE35 2168252 c.2361G>A synonymous_variant 0.14
PPE35 2170503 c.109dupG frameshift_variant 0.18
Rv1979c 2221980 c.1185A>G synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289080 c.162G>T synonymous_variant 0.12
pncA 2290209 c.-969delG upstream_gene_variant 0.29
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726681 c.491_492dupTG frameshift_variant 0.25
thyA 3074018 p.Phe152Leu missense_variant 0.12
thyA 3074027 p.Phe149Ile missense_variant 0.12
thyA 3074035 p.Cys146Ser missense_variant 0.12
thyA 3074060 p.Ile138Phe missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087308 c.489G>T synonymous_variant 0.13
fbiD 3339304 p.Thr63Pro missense_variant 0.4
Rv3083 3448310 c.-194G>A upstream_gene_variant 0.29
Rv3083 3449274 c.771C>A synonymous_variant 0.11
Rv3083 3449690 p.Thr396Asn missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612470 p.Glu216Gly missense_variant 0.15
fbiA 3640531 c.-12C>T upstream_gene_variant 0.25
fbiB 3641672 c.138G>T synonymous_variant 0.15
embC 4240950 p.Val363Ala missense_variant 0.29
embC 4242049 c.2187C>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246292 c.-222A>C upstream_gene_variant 0.11
embB 4248138 p.Gly542Asp missense_variant 0.14
aftB 4268226 p.Ala204Gly missense_variant 0.11
aftB 4268324 c.512delT frameshift_variant 0.12
ethA 4327263 p.Gly71Arg missense_variant 0.11
ethA 4328423 c.-950T>C upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338699 c.-179delT upstream_gene_variant 0.33
gid 4407986 p.Gly73Arg missense_variant 0.14