TB-Profiler result

Run: ERR038280
Summary

Run ID: ERR038280

Sample name:

Date: 31-03-2023 08:39:48

Number of reads: 15073420

Percentage reads mapped: 99.29

Strain: lineage3

Drug-resistance: Other

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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
lineage3 East-African-Indian CAS RD750 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
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762249 p.Leu815Val missense_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_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 0.15
mmpL5 777820 c.661C>T synonymous_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304676 c.1746A>C synonymous_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.23
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168651 p.Leu654Phe missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.19
PPE35 2169866 c.747G>C synonymous_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.27
eis 2715586 c.-254G>C upstream_gene_variant 0.46
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.21
pepQ 2860399 p.Arg7Gln missense_variant 1.0
Rv2752c 3064552 p.Arg547Pro missense_variant 0.23
thyA 3073806 c.666C>G synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.21
fbiB 3642734 c.1200G>C synonymous_variant 0.23
fbiB 3642772 p.Asp413Ala missense_variant 0.25
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.18
clpC1 4039932 p.Gly258Val missense_variant 0.39
embC 4239842 c.-21C>A upstream_gene_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.17
embC 4242476 p.Pro872Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.37
ubiA 4269529 p.Ala102Gly missense_variant 0.27
ethA 4327672 c.-199G>A upstream_gene_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0