TB-Profiler result

Run: SRR6045028
Summary

Run ID: SRR6045028

Sample name:

Date: 04-04-2023 11:51:37

Number of reads: 187529

Percentage reads mapped: 9.25

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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8423 c.1122G>A synonymous_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9075 p.Arg592Cys missense_variant 0.29
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620583 c.693G>C synonymous_variant 0.29
ccsA 620586 c.696C>G synonymous_variant 0.29
ccsA 620598 c.708C>G synonymous_variant 0.22
ccsA 620601 c.711C>T synonymous_variant 0.22
ccsA 620604 c.714C>G synonymous_variant 0.22
ccsA 620607 c.717T>C synonymous_variant 0.22
ccsA 620613 c.723C>G synonymous_variant 0.22
ccsA 620622 c.732G>C synonymous_variant 0.25
ccsA 620625 c.735A>C synonymous_variant 0.25
ccsA 620631 c.741T>G synonymous_variant 0.25
ccsA 620646 c.756G>A synonymous_variant 0.25
ccsA 620649 c.759A>G synonymous_variant 0.25
ccsA 620659 c.769_771delCGCinsAGG synonymous_variant 0.25
ccsA 620664 c.774C>T synonymous_variant 0.25
ccsA 620682 c.792G>A synonymous_variant 0.25
ccsA 620688 c.798G>C synonymous_variant 0.22
rpoB 760608 c.802C>T synonymous_variant 0.29
rpoB 760722 p.Gly306Ser missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764086 c.717C>T synonymous_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
rpsL 781637 c.78C>A synonymous_variant 0.67
fbiC 1302890 c.-41G>T upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169105 p.Leu503Ser missense_variant 0.4
Rv1979c 2222241 c.924C>T synonymous_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222773 p.Glu131Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714753 p.Gln194* stop_gained 1.0
eis 2714891 p.Arg148Ser missense_variant 0.33
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747683 c.-85A>T upstream_gene_variant 0.5
pepQ 2860485 c.-67C>G upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040677 p.Arg10Ser missense_variant 0.25
clpC1 4040788 c.-84C>A upstream_gene_variant 0.14
panD 4044314 c.-33C>T upstream_gene_variant 0.5
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241643 p.Ala594Glu missense_variant 0.67
embC 4241847 p.Thr662Asn missense_variant 0.67
embC 4242202 c.2340C>T synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246044 p.Val938Leu missense_variant 0.33
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248002 p.Gln497* stop_gained 0.67
embB 4249738 c.3225C>A synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269777 p.Lys19Asn missense_variant 0.4
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys 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