TB-Profiler result

Run: ERR4816639
Summary

Run ID: ERR4816639

Sample name:

Date: 01-04-2023 14:32:37

Number of reads: 476708

Percentage reads mapped: 99.12

Strain: lineage1.1.2

Drug-resistance: Other

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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 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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
gid 4407944 p.Gln87* stop_gained 1.0 streptomycin
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
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7986 p.Pro229Ser missense_variant 0.25
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 490584 c.-199C>A upstream_gene_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 760667 p.Gln287His missense_variant 0.17
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 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 776969 p.Gln504His missense_variant 0.2
mmpL5 777213 c.1267delG frameshift_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801093 p.Tyr95* stop_gained 0.11
fbiC 1305169 c.2240delA frameshift_variant 0.11
Rv1258c 1406504 c.837C>T synonymous_variant 1.0
Rv1258c 1406592 p.Tyr250Phe missense_variant 0.11
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674050 p.Gln204Arg missense_variant 0.22
inhA 1674467 p.Asp89Gly missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101955 p.Gln363Ser missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156131 c.-20C>T upstream_gene_variant 0.13
katG 2156288 c.-177A>T upstream_gene_variant 0.17
PPE35 2167701 p.Ala971Gly missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169319 p.Phe432Leu missense_variant 0.18
PPE35 2170518 c.94delG frameshift_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289613 c.-372T>C upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746199 p.Val467Ala missense_variant 0.2
ribD 2987525 c.687G>T synonymous_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448532 p.Ile10Thr missense_variant 0.14
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474539 p.Ile178Thr missense_variant 0.18
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568864 c.-185G>A upstream_gene_variant 0.13
rpoA 3877653 c.855C>T synonymous_variant 0.29
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239673 c.-190T>C upstream_gene_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240743 p.Asp294Gly missense_variant 0.14
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 4243939 p.Trp236* stop_gained 0.14
embA 4245218 c.1986C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268479 p.Ala120Thr missense_variant 0.33
ubiA 4269031 p.Gly268Asp missense_variant 1.0
ubiA 4269104 p.Ser244Gly missense_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327188 p.Arg96Gly missense_variant 0.12
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 4407790 p.Ala138Val missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408116 c.87C>T synonymous_variant 1.0