TB-Profiler result

Run: ERR046898
Summary

Run ID: ERR046898

Sample name:

Date: 31-03-2023 08:56:11

Number of reads: 4614614

Percentage reads mapped: 99.22

Strain: lineage1.2.2.1

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 0.98
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 Indo-Oceanic NA RD239 0.99
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 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8377 p.Asp359Gly missense_variant 0.15
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 1.0
mshA 575932 p.Glu195Asp missense_variant 0.24
rpoB 759620 c.-187A>C upstream_gene_variant 0.32
rpoC 762836 c.-534C>G upstream_gene_variant 0.38
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 764725 p.Phe452Leu missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416450 p.Gly300Cys missense_variant 1.0
embR 1416937 p.His137Gln missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417233 c.115C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.19
ndh 2102891 p.Phe51Ser missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167871 c.2742G>C synonymous_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168205 p.Pro803Gln missense_variant 1.0
PPE35 2169379 p.Phe412Val missense_variant 0.2
PPE35 2169866 c.747G>C synonymous_variant 0.38
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
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 0.26
eis 2715586 c.-254G>C upstream_gene_variant 0.27
ahpC 2725954 c.-239C>T upstream_gene_variant 0.24
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726114 c.-79C>T upstream_gene_variant 1.0
ahpC 2726756 c.564C>G synonymous_variant 0.26
folC 2746186 c.1413G>C synonymous_variant 0.21
Rv2752c 3064741 p.Gly484Ala missense_variant 0.28
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
fprA 3475280 p.Val425Gly missense_variant 0.27
Rv3236c 3612804 p.Ala105Thr missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.36
fbiB 3642734 c.1200G>C synonymous_variant 0.23
alr 3840268 p.Thr385Pro missense_variant 0.29
ddn 3987013 p.Gly57Ala missense_variant 0.2
clpC1 4039363 p.Ala448Pro missense_variant 0.19
clpC1 4039932 p.Gly258Val missense_variant 0.23
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044307 c.-26A>G upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.28
embC 4241456 p.Ala532Pro missense_variant 0.36
embC 4242425 p.Arg855Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.37
embC 4242827 p.Leu989Val missense_variant 0.23
embA 4243532 c.300C>A synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246275 p.Ala1015Thr missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248725 p.Ser738Ala missense_variant 0.24
ubiA 4269387 p.Glu149Asp missense_variant 0.99
ubiA 4269469 p.Pro122Gln missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.24
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407532 p.Ala224Gly missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408124 p.Ala27Pro missense_variant 1.0