TB-Profiler result

Run: SRR18213767
Summary

Run ID: SRR18213767

Sample name:

Date: 03-04-2023 19:28:28

Number of reads: 3477817

Percentage reads mapped: 99.15

Strain: lineage1.1.3

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.99
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 5195 c.-45C>G upstream_gene_variant 1.0
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.24
fgd1 491448 c.666C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 576280 c.933A>C synonymous_variant 0.98
mshA 576675 p.Arg443His missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.98
rpoC 763886 c.517C>A synonymous_variant 0.98
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.15
mmpL5 778099 p.Asp128Asn missense_variant 0.99
mmpS5 778581 p.Gly109Ser missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.18
fbiC 1304159 p.Val410Gly missense_variant 0.27
fbiC 1304166 c.1236A>G synonymous_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
inhA 1673406 c.-796C>T upstream_gene_variant 1.0
inhA 1674082 c.-120G>A upstream_gene_variant 1.0
inhA 1674966 c.765T>G synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154556 p.Arg519His missense_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.98
PPE35 2170584 p.Ile10Ser missense_variant 0.98
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.99
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
ahpC 2726338 p.Val49Gly missense_variant 0.3
ahpC 2726341 p.Val50Gly missense_variant 0.21
ahpC 2726350 p.Trp53Leu missense_variant 0.16
pepQ 2859904 p.Val172Gly missense_variant 0.19
ribD 2987323 p.Val162Gly missense_variant 0.31
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3068043 c.-98A>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.18
ald 3086767 c.-53A>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086853 p.Asn12Asp missense_variant 1.0
fbiD 3339153 p.Leu12Phe missense_variant 0.21
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.16
embC 4240153 c.291G>A synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245314 c.2082G>C synonymous_variant 0.96
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247057 p.Arg182Cys missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.98
aftB 4269606 c.-770T>C upstream_gene_variant 0.97
whiB6 4338308 c.213dupT frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0