TB-Profiler result

Run: SRR22424893
Summary

Run ID: SRR22424893

Sample name:

Date: 04-04-2023 04:15:50

Number of reads: 1062247

Percentage reads mapped: 99.2

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304477 p.Ala516Glu missense_variant 1.0
Rv1258c 1406242 p.Ala367Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472294 n.449G>T non_coding_transcript_exon_variant 0.29
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.67
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.8
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.8
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.8
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.8
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.8
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.67
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.67
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.4
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.8
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.75
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.75
rrl 1473449 n.-209G>A upstream_gene_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.5
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.5
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.5
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.5
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.5
inhA 1674406 p.Glu69Gln missense_variant 0.15
inhA 1674419 p.Ser73Asn missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167758 p.Gly952Asp missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168254 p.Pro787Ser missense_variant 0.2
PPE35 2168485 p.Asn710Asp missense_variant 0.11
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2170109 c.504C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612566 p.Gly184Asp missense_variant 0.1
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267845 p.Gly331Val missense_variant 0.12
aftB 4268526 p.Arg104Gln missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407758 p.Ser149Arg missense_variant 1.0