TB-Profiler result

Run: ERR2513092
Summary

Run ID: ERR2513092

Sample name:

Date: 31-03-2023 19:27:23

Number of reads: 538079

Percentage reads mapped: 99.33

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 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.3 Indo-Oceanic EAI6 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 5436 p.Asn66Ser missense_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6278 p.Gly347Ser missense_variant 0.13
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 9077 c.1776C>T synonymous_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.19
fgd1 491334 c.552C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575589 p.Arg81Leu missense_variant 0.15
ccsA 619831 c.-60T>G upstream_gene_variant 0.33
rpoB 761152 p.Leu449Gln missense_variant 0.13
rpoB 761999 c.2193G>C synonymous_variant 0.11
rpoB 762008 c.2202C>G synonymous_variant 0.12
rpoB 762014 c.2208C>T synonymous_variant 0.12
rpoB 762017 c.2211A>G synonymous_variant 0.12
rpoB 762086 c.2280G>C synonymous_variant 0.11
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
rpoC 765230 p.Ala621Thr missense_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 781458 c.-102C>T upstream_gene_variant 1.0
Rv1258c 1407488 c.-148C>T upstream_gene_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.11
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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169821 c.792C>T synonymous_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289949 c.-708A>G upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2860116 c.303G>A synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065540 p.Val218Leu missense_variant 1.0
thyX 3067673 p.His91Gln missense_variant 0.11
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
whiB7 3568502 p.Ala60Thr missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040728 c.-24G>T upstream_gene_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.25
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 4244217 p.Thr329Ala missense_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327315 c.-234A>T upstream_gene_variant 0.13
whiB6 4338243 c.278delG frameshift_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 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0