TB-Profiler result

Run: ERR046896
Summary

Run ID: ERR046896

Sample name:

Date: 31-03-2023 08:56:06

Number of reads: 4859262

Percentage reads mapped: 99.07

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 9047 c.1746C>T synonymous_variant 0.99
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.29
mshA 575932 p.Glu195Asp missense_variant 0.29
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.28
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.39
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
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406358 p.Ile328Thr missense_variant 0.2
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.15
rrs 1471658 n.-188T>G upstream_gene_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474424 n.767C>T non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167871 c.2742G>C synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.28
PPE35 2170156 p.Ala153Pro missense_variant 0.21
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 0.28
eis 2715586 c.-254G>C upstream_gene_variant 0.39
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746186 c.1413G>C synonymous_variant 0.25
Rv2752c 3064552 p.Arg547Pro missense_variant 0.19
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064741 p.Gly484Ala missense_variant 0.29
Rv2752c 3065265 c.927C>G synonymous_variant 0.25
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
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 0.28
fbiB 3641955 p.Gly141Arg missense_variant 0.2
rpoA 3878238 p.Asp90Glu missense_variant 0.15
ddn 3987013 p.Gly57Ala missense_variant 0.26
clpC1 4038857 c.1848C>A synonymous_variant 0.16
clpC1 4039363 p.Ala448Pro missense_variant 0.28
clpC1 4039932 p.Gly258Val missense_variant 0.31
clpC1 4040517 p.Val63Ala missense_variant 0.99
clpC1 4040738 c.-34G>T upstream_gene_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242476 p.Pro872Ala missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.32
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244375 c.1143C>G synonymous_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 0.99
embB 4247646 p.Glu378Ala missense_variant 0.98
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
ethR 4326994 c.-555C>T upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.23
ethR 4327912 p.Arg122Gly missense_variant 0.18
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 0.99