TB-Profiler result

Run: SRR18213863
Summary

Run ID: SRR18213863

Sample name:

Date: 03-04-2023 19:32:20

Number of reads: 3453707

Percentage reads mapped: 99.42

Strain: lineage1.2.1.1

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 0.99
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.98
lineage1.2.1.1 Indo-Oceanic NA RD239 0.98
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 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.95
gyrA 9143 c.1842T>C synonymous_variant 0.98
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.98
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775746 p.Met912Thr missense_variant 0.97
mmpL5 776100 p.Thr794Ile missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303858 p.Gly310* stop_gained 0.95
fbiC 1304159 p.Val410Gly missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 0.97
atpE 1460853 c.-192T>G upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674966 c.765T>G synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153933 p.Ala727Ser missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 0.99
katG 2155144 p.Asn323Ser missense_variant 0.95
PPE35 2167926 p.Leu896Ser missense_variant 0.98
PPE35 2168533 p.Val694Leu missense_variant 0.94
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290129 c.-888C>A upstream_gene_variant 0.97
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519035 c.921C>T synonymous_variant 0.98
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
ahpC 2726338 p.Val49Gly missense_variant 0.22
ahpC 2726341 p.Val50Gly missense_variant 0.22
ribD 2987323 p.Val162Gly missense_variant 0.19
thyA 3073806 c.666C>G synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 0.96
Rv3083 3448714 p.Asp71His missense_variant 0.99
Rv3083 3448835 p.Ser111Ile missense_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.97
fprA 3475159 p.Asn385Asp missense_variant 0.97
fbiB 3640557 c.-978T>C upstream_gene_variant 0.99
clpC1 4040517 p.Val63Ala missense_variant 0.98
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 0.98
embA 4244610 p.Ala460Thr missense_variant 0.96
embA 4245969 p.Pro913Ser missense_variant 0.98
embB 4247646 p.Glu378Ala missense_variant 0.99
embB 4248515 p.Val668Ile missense_variant 0.95
embB 4249352 c.2839C>A synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.99
aftB 4269606 c.-770T>C upstream_gene_variant 0.98
ethR 4327360 c.-189C>G upstream_gene_variant 0.99
whiB6 4338361 p.Arg54Gln missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.97
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.98
gid 4407995 p.Ser70Arg missense_variant 1.0