TB-Profiler result

Run: ERR1194804
Summary

Run ID: ERR1194804

Sample name:

Date: 31-03-2023 12:34:08

Number of reads: 856447

Percentage reads mapped: 99.54

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
tlyA 1917979 c.44delG frameshift_variant 0.17 capreomycin
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 491732 p.Gln317Arg missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763976 p.Arg203Ser missense_variant 0.12
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766689 p.Val1107Ala missense_variant 0.1
rpoC 766712 p.Ser1115Thr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779673 c.-768A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917826 c.-114A>C upstream_gene_variant 0.33
tlyA 1917874 c.-66G>A upstream_gene_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102317 c.726A>G synonymous_variant 0.12
ndh 2102590 c.453A>T synonymous_variant 0.14
ndh 2103084 c.-42T>A upstream_gene_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 0.95
PPE35 2167764 p.Ile950Lys missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168361 p.Ile751Asn missense_variant 0.22
PPE35 2168908 p.Thr569Ala missense_variant 0.11
PPE35 2170510 p.Ala35Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223320 c.-156T>G upstream_gene_variant 0.31
folC 2746745 p.Val285Gly missense_variant 0.18
pepQ 2859390 c.1029A>T synonymous_variant 0.15
ribD 2987615 c.777A>G stop_lost&splice_region_variant 0.11
Rv2752c 3064566 c.1626G>C synonymous_variant 0.5
Rv2752c 3065500 p.Gly231Val missense_variant 1.0
Rv2752c 3067076 c.-885A>C upstream_gene_variant 0.24
thyA 3074544 c.-73T>G upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339274 p.Val53Leu missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878490 c.18C>G synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243464 p.Ala78Pro missense_variant 0.11
aftB 4267564 p.Thr425Pro missense_variant 0.21
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0