TB-Profiler result

Run: ERR1194812
Summary

Run ID: ERR1194812

Sample name:

Date: 31-03-2023 12:34:29

Number of reads: 656128

Percentage reads mapped: 99.09

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 0.99
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
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 5791 p.Glu184Asp missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8988 p.Thr563Ala missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.43
mshA 576535 c.1188T>G synonymous_variant 0.4
ccsA 619913 p.Val8Gly missense_variant 0.29
ccsA 619955 p.Val22Gly missense_variant 0.29
ccsA 620298 c.408G>A synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 762283 p.Val826Gly missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763848 p.Lys160Thr missense_variant 0.22
rpoC 763917 p.Glu183Ala missense_variant 0.22
rpoC 765445 c.2076G>T synonymous_variant 0.17
rpoC 766428 p.Val1020Gly missense_variant 0.43
rpoC 766641 p.His1091Leu missense_variant 0.22
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779132 p.Pro48His missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303519 p.Ser197Arg missense_variant 0.18
Rv1258c 1406238 p.Gly368Asp missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416498 p.Ser284Ala missense_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473396 n.-262A>T upstream_gene_variant 0.91
inhA 1674624 c.423A>G synonymous_variant 0.2
inhA 1674960 c.759C>A synonymous_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834861 c.1320G>T synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918718 p.Val260Glu missense_variant 0.22
katG 2154161 p.Glu651Gln missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156284 c.-173C>T upstream_gene_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168882 c.1731T>A synonymous_variant 0.17
PPE35 2169056 c.1557A>T synonymous_variant 0.22
PPE35 2169886 p.Gly243Cys missense_variant 0.67
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170147 p.Ser156Ala missense_variant 0.29
PPE35 2170159 p.Ala152Ser missense_variant 0.29
Rv1979c 2222203 p.Phe321Cys missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289753 c.-512T>C upstream_gene_variant 1.0
kasA 2518541 p.Gln143* stop_gained 0.29
folC 2746628 p.Asp324Ala missense_variant 0.25
folC 2747066 p.Gly178Asp missense_variant 0.22
folC 2747491 p.Gln36His missense_variant 0.29
Rv2752c 3065305 p.Ala296Val missense_variant 0.25
Rv2752c 3065500 p.Gly231Val missense_variant 1.0
Rv2752c 3066186 p.Asp2Glu missense_variant 0.17
Rv2752c 3066335 c.-144T>G upstream_gene_variant 0.22
Rv2752c 3066359 c.-168G>T upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613189 c.-73G>A upstream_gene_variant 0.4
fbiB 3640566 c.-969T>G upstream_gene_variant 0.22
clpC1 4039404 p.Glu434Val missense_variant 0.4
embC 4240251 p.Leu130Gln missense_variant 0.2
embC 4241032 c.1172delC frameshift_variant 0.22
embC 4241539 c.1677T>G synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243824 p.Thr198Ser missense_variant 0.67
embA 4244905 p.Val558Gly missense_variant 0.29
embB 4248902 p.Thr797Pro missense_variant 0.25
embB 4249113 p.Lys867Thr missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269247 p.Leu196Arg missense_variant 0.67
ubiA 4269716 p.Leu40Val missense_variant 0.2
ubiA 4269799 p.Asn12Thr missense_variant 0.29
ubiA 4269840 c.-7A>G upstream_gene_variant 0.33
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