TB-Profiler result

Run: ERR245836
Summary

Run ID: ERR245836

Sample name:

Date: 31-03-2023 18:24:07

Number of reads: 9996901

Percentage reads mapped: 98.8

Strain: lineage1.2.2

Drug-resistance: MDR-TB

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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
lineage1.2.2 Indo-Oceanic EAI1 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
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 0.99 streptomycin
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
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 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8445 p.Arg382Gly missense_variant 0.23
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759831 p.Thr9Pro missense_variant 0.24
rpoC 762836 c.-534C>G upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763552 c.183C>T synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.99
rpoC 763886 c.517C>A synonymous_variant 0.99
rpoC 767305 p.Tyr1312* stop_gained 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.19
mmpS5 779625 c.-720G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.99
embR 1417136 p.Ser71Ile missense_variant 0.19
embR 1417501 c.-154A>C upstream_gene_variant 0.28
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.24
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.18
fabG1 1673449 p.Thr4Pro missense_variant 0.37
inhA 1674892 p.Asn231Asp missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.38
PPE35 2170156 p.Ala153Pro missense_variant 0.28
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 0.22
eis 2715586 c.-254G>C upstream_gene_variant 0.57
ahpC 2725954 c.-239C>T upstream_gene_variant 0.27
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746186 c.1413G>C synonymous_variant 0.29
pepQ 2859381 c.1038C>G synonymous_variant 0.21
Rv2752c 3064741 p.Gly484Ala missense_variant 0.21
thyA 3073817 p.Gln219Glu missense_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.28
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
Rv3236c 3611982 p.Ala379Pro missense_variant 0.34
fbiB 3641955 p.Gly141Arg missense_variant 0.15
fbiB 3642734 c.1200G>C synonymous_variant 0.26
clpC1 4038328 p.Glu793Gln missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.19
clpC1 4039363 p.Ala448Pro missense_variant 0.26
clpC1 4039932 p.Gly258Val missense_variant 0.31
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.25
embC 4241128 c.1266G>C synonymous_variant 0.27
embC 4241429 p.Phe523Val missense_variant 0.42
embC 4241456 p.Ala532Pro missense_variant 0.44
embC 4242425 p.Arg855Gly missense_variant 0.15
embC 4242476 p.Pro872Ala missense_variant 0.25
embA 4242559 c.-674G>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.3
embA 4245670 p.Ala813Gly missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246979 p.Gly156Cys missense_variant 1.0
embB 4247603 p.Leu364Val missense_variant 0.24
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267960 p.Val293Met missense_variant 1.0
ubiA 4269162 p.Leu224Phe missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.19
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.37
ethR 4327912 p.Arg122Gly missense_variant 0.23
whiB6 4338203 p.Arg107Cys missense_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 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0