TB-Profiler result

Run: ERR279559
Summary

Run ID: ERR279559

Sample name:

Date: 31-03-2023 23:41:07

Number of reads: 4192132

Percentage reads mapped: 99.4

Strain: lineage4.3.2.1;lineage1.2.2.2

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
lineage4 Euro-American LAM;T;S;X;H None 0.32
lineage1 Indo-Oceanic EAI RD239 0.66
lineage4.3 Euro-American (LAM) mainly-LAM None 0.33
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.66
lineage4.3.2 Euro-American (LAM) LAM3 None 0.32
lineage1.2.2.2 Indo-Oceanic NA RD239 0.63
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.33
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 0.64
gyrB 5520 p.Pro94Leu missense_variant 0.38
gyrB 6112 p.Met291Ile missense_variant 0.69
gyrA 7222 c.-80C>T upstream_gene_variant 0.27
gyrA 7268 c.-34C>T upstream_gene_variant 0.69
gyrA 7359 p.Ile20Val missense_variant 0.71
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.68
gyrA 9143 c.1842T>C synonymous_variant 0.74
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491394 c.612C>T synonymous_variant 0.71
fgd1 491742 c.960T>C synonymous_variant 0.75
rpoC 763031 c.-339T>C upstream_gene_variant 0.73
rpoC 763552 c.183C>T synonymous_variant 0.7
rpoC 763884 p.Ala172Val missense_variant 0.64
rpoC 763886 c.517C>A synonymous_variant 0.66
rpoC 764995 c.1626C>G synonymous_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.65
mmpS5 779625 c.-720G>A upstream_gene_variant 0.68
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.68
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.68
katG 2154724 p.Arg463Leu missense_variant 0.72
PPE35 2167926 p.Leu896Ser missense_variant 0.66
PPE35 2168742 p.Gly624Asp missense_variant 0.74
PPE35 2169427 p.Pro396Thr missense_variant 0.64
Rv1979c 2222098 p.Thr356Lys missense_variant 0.63
Rv1979c 2222308 p.Asp286Gly missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290107 c.-866T>A upstream_gene_variant 0.3
kasA 2518132 c.18C>T synonymous_variant 0.67
ahpC 2726051 c.-142G>A upstream_gene_variant 0.7
thyA 3073868 p.Thr202Ala missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.69
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.73
fprA 3475159 p.Asn385Asp missense_variant 0.77
clpC1 4038287 c.2418C>T synonymous_variant 0.31
clpC1 4040517 p.Val63Ala missense_variant 0.68
clpC1 4040719 c.-15A>G upstream_gene_variant 0.71
embC 4240671 p.Thr270Ile missense_variant 0.67
embC 4241042 p.Asn394Asp missense_variant 0.67
embC 4242425 p.Arg855Gly missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245670 p.Ala813Gly missense_variant 0.67
embA 4245969 p.Pro913Ser missense_variant 0.57
embB 4246979 p.Gly156Cys missense_variant 0.73
embB 4247646 p.Glu378Ala missense_variant 0.63
aftB 4267960 p.Val293Met missense_variant 0.78
ubiA 4269387 p.Glu149Asp missense_variant 0.71
aftB 4269606 c.-770T>C upstream_gene_variant 0.73
ethA 4326148 c.1326G>T synonymous_variant 0.68
ethA 4326439 p.Asn345Lys missense_variant 0.65
whiB6 4338203 p.Arg107Cys missense_variant 0.55
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.63
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407848 p.Ala119Thr missense_variant 0.76
gid 4407873 c.330G>T synonymous_variant 0.78
gid 4408156 p.Leu16Arg missense_variant 0.36