TB-Profiler result

Run: ERR046978
Summary

Run ID: ERR046978

Sample name:

Date: 31-03-2023 08:59:35

Number of reads: 4692292

Percentage reads mapped: 99.16

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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.32
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.22
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 777399 p.Thr361Arg missense_variant 0.22
mmpL5 778042 p.Ala147Ser missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.27
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.31
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.23
inhA 1674892 p.Asn231Asp missense_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.99
PPE35 2169866 c.747G>C synonymous_variant 0.39
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 2714366 p.Val323Leu missense_variant 0.31
eis 2715016 p.Arg106His missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
pepQ 2860398 c.21A>C synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064741 p.Gly484Ala missense_variant 0.34
thyX 3067995 c.-50A>C upstream_gene_variant 0.23
thyA 3073806 c.666C>G synonymous_variant 0.17
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
fbiB 3642734 c.1200G>C synonymous_variant 0.16
rpoA 3878238 p.Asp90Glu missense_variant 0.17
ddn 3987013 p.Gly57Ala missense_variant 0.23
clpC1 4038857 c.1848C>A synonymous_variant 0.23
clpC1 4039932 p.Gly258Val missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241395 p.Lys511Asn missense_variant 1.0
embC 4241456 p.Ala532Pro missense_variant 0.36
embC 4242476 p.Pro872Ala missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.35
embC 4242827 p.Leu989Val missense_variant 0.2
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.23
aftB 4269606 c.-770T>C upstream_gene_variant 0.99
ethA 4327672 c.-199G>A upstream_gene_variant 0.32
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