TB-Profiler result

Run: SRR12199427
Summary

Run ID: SRR12199427

Sample name:

Date: 03-04-2023 06:39:03

Number of reads: 264624

Percentage reads mapped: 50.69

Strain: lineage1

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
lineage1 Indo-Oceanic EAI RD239 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
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576408 p.Ser354* stop_gained 0.33
mshA 576410 p.Phe355Leu missense_variant 0.4
rpoB 759638 c.-169_-168insA upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 779331 c.-851C>T upstream_gene_variant 0.67
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406676 p.Leu222Pro missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.33
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.33
fabG1 1673285 c.-155A>G upstream_gene_variant 0.4
fabG1 1673380 c.-60C>G upstream_gene_variant 0.44
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170035 p.Val193Ala missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.75
PPE35 2170053 p.Thr187Ser missense_variant 0.75
PPE35 2170385 c.228G>T synonymous_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289524 c.-283C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.4
thyA 3073793 p.Tyr227Asn missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449213 p.Arg237Leu missense_variant 0.4
Rv3083 3449469 p.Glu322Asp missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.83
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.42
ddn 3986815 c.-29G>T upstream_gene_variant 0.25
clpC1 4038332 c.2373C>T synonymous_variant 0.25
clpC1 4038722 c.1983G>A synonymous_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241008 c.1146G>A synonymous_variant 0.15
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241607 p.Thr582Asn missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247427 p.Gly305Ala missense_variant 0.15
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.89
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0