TB-Profiler result

Run: SRR6256987
Summary

Run ID: SRR6256987

Sample name:

Date: 04-04-2023 13:22:01

Number of reads: 976089

Percentage reads mapped: 100.0

Strain: lineage2.2.1

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
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6936 p.Pro566Gln missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8055 p.Arg252Gly missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490652 c.-131G>T upstream_gene_variant 0.17
fgd1 490786 p.Ala2Ser missense_variant 0.29
fgd1 491394 c.612C>G synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575850 p.Arg168Leu missense_variant 0.18
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576098 p.Asp251Ser missense_variant 1.0
mshA 576102 p.Arg252Pro missense_variant 1.0
mshA 576104 p.Arg253Ser missense_variant 1.0
mshA 576521 p.Gly392Trp missense_variant 0.14
ccsA 620075 p.Gly62Val missense_variant 0.18
ccsA 620169 c.279G>T synonymous_variant 0.13
ccsA 620551 p.Asp221Tyr missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620791 p.Val301Leu missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766485 p.Val1039Ala missense_variant 1.0
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
mmpL5 777473 c.1008T>C synonymous_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302987 c.57C>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471652 n.-194G>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471758 n.-88G>T upstream_gene_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834868 p.Arg443Ser missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102361 p.Leu228Ile missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168497 p.Ile706Val missense_variant 0.1
PPE35 2169114 p.Ala500Gly missense_variant 0.11
PPE35 2169856 p.Gly253Cys missense_variant 0.12
PPE35 2170411 p.Ala68Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289891 c.-650G>T upstream_gene_variant 0.12
eis 2714777 p.Val186Leu missense_variant 0.12
eis 2714788 p.Trp182Leu missense_variant 0.13
eis 2714842 p.Arg164Leu missense_variant 0.14
eis 2715503 c.-171G>T upstream_gene_variant 0.15
ahpC 2726338 p.Val49Gly missense_variant 0.27
folC 2747089 c.510G>T synonymous_variant 0.12
ribD 2987340 p.Asp168Tyr missense_variant 0.14
Rv2752c 3066270 c.-79G>A upstream_gene_variant 0.12
thyX 3068005 c.-60G>T upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087256 p.Ala146Asp missense_variant 0.12
fbiD 3339328 p.Ala71Ser missense_variant 0.13
fbiD 3339744 c.627A>G synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474937 p.Glu311* stop_gained 0.25
fprA 3474952 p.Gln316Lys missense_variant 0.2
Rv3236c 3612420 p.Ala233Ser missense_variant 0.14
Rv3236c 3612794 p.Gly108Val missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640455 c.-88C>A upstream_gene_variant 0.25
fbiB 3641727 p.Glu65* stop_gained 0.14
fbiB 3642303 p.Gln257* stop_gained 0.15
fbiB 3642350 c.816G>T synonymous_variant 0.14
ddn 3986964 p.Phe41Leu missense_variant 0.12
clpC1 4039420 p.Ala429Ser missense_variant 0.13
clpC1 4040179 p.Arg176Ser missense_variant 0.12
embC 4241569 c.1707C>T synonymous_variant 0.15
embC 4241586 p.Ser575Phe missense_variant 0.14
embC 4241602 p.Met580Ile missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246374 p.Gly1048Trp missense_variant 0.15
embB 4247148 p.Thr212Ile missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268815 c.22C>T synonymous_variant 0.13
ubiA 4269868 c.-37_-36delCG upstream_gene_variant 0.15
ubiA 4269872 c.-39G>A upstream_gene_variant 0.15
ubiA 4269986 c.-153G>T upstream_gene_variant 0.22
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