TB-Profiler result

Run: ERR245742
Summary

Run ID: ERR245742

Sample name:

Date: 31-03-2023 18:18:30

Number of reads: 7283432

Percentage reads mapped: 99.11

Strain: lineage1.1.2

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
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
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 7493 c.192C>T synonymous_variant 0.24
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 491742 c.960T>C synonymous_variant 0.99
ccsA 620407 p.Pro173Ala missense_variant 0.26
rpoB 759831 p.Thr9Pro missense_variant 0.32
rpoC 762836 c.-534C>G upstream_gene_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.99
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 777399 p.Thr361Arg missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.2
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.26
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.27
fabG1 1673283 c.-157A>C upstream_gene_variant 1.0
inhA 1674892 p.Asn231Asp missense_variant 0.24
tlyA 1917777 c.-163A>G upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918106 p.Thr56Ile missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155557 c.555C>T synonymous_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.41
PPE35 2170378 p.Ala79Thr missense_variant 1.0
Rv1979c 2221783 p.Ala461Glu missense_variant 1.0
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 1.0
eis 2714199 p.Lys378Asn missense_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.22
eis 2715586 c.-254G>C upstream_gene_variant 0.53
ahpC 2725954 c.-239C>T upstream_gene_variant 0.23
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726672 c.480G>A synonymous_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.21
Rv2752c 3064632 c.1560C>T synonymous_variant 0.99
Rv2752c 3064741 p.Gly484Ala missense_variant 0.22
thyX 3067995 c.-50A>C upstream_gene_variant 0.18
thyA 3073806 c.666C>G synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448442 c.-62A>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.99
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613012 c.105G>A synonymous_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.19
clpC1 4038857 c.1848C>A synonymous_variant 0.18
clpC1 4039932 p.Gly258Val missense_variant 0.36
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241429 p.Phe523Val missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.46
embC 4242827 p.Leu989Val missense_variant 0.27
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245166 p.Pro645Gln missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.99
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249504 p.Gln997His missense_variant 0.26
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.24
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.2
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 4407873 c.330G>T synonymous_variant 1.0