TB-Profiler result

Run: SRR21277771
Summary

Run ID: SRR21277771

Sample name:

Date: 04-04-2023 01:40:44

Number of reads: 14646551

Percentage reads mapped: 97.74

Strain: lineage2.2.1.2

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
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
lineage2.2.1.2 East-Asian (Beijing) Beijing-RD142 RD105;RD207;RD181;RD142 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7554 p.His85Asn missense_variant 0.1
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490674 c.-109G>A upstream_gene_variant 0.11
fgd1 490692 c.-91C>T upstream_gene_variant 0.14
fgd1 490694 c.-89G>T upstream_gene_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575397 p.Arg17His missense_variant 0.13
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575923 c.576C>T synonymous_variant 0.18
mshA 575924 p.Gly193* stop_gained 0.19
mshA 576115 c.768G>A synonymous_variant 0.11
mshA 576253 c.906G>T synonymous_variant 0.17
mshA 576256 c.909C>T synonymous_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764550 p.Pro394Gln missense_variant 0.1
rpoC 764603 p.Arg412Trp missense_variant 0.11
rpoC 766117 c.2748C>T synonymous_variant 0.23
rpoC 766970 p.Ala1201Thr missense_variant 0.12
mmpL5 775620 p.Ser954* stop_gained 0.13
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777284 c.1197C>T synonymous_variant 0.11
mmpL5 777387 p.Gly365Asp missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801230 p.Ala141Asp missense_variant 0.11
rplC 801232 p.Gln142Lys missense_variant 0.2
rplC 801264 c.456C>T synonymous_variant 0.11
fbiC 1303102 p.Leu58Met missense_variant 0.17
fbiC 1304464 p.Gly512Cys missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99
Rv1258c 1406971 p.Arg124Cys missense_variant 0.17
Rv1258c 1407500 c.-160C>T upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674822 c.621C>A synonymous_variant 0.17
rpsA 1833355 c.-187C>T upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917953 p.Ala5Asp missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918568 p.Ala210Glu missense_variant 0.12
tlyA 1918602 c.663C>T synonymous_variant 0.12
ndh 2101686 p.Gln453* stop_gained 0.12
ndh 2102371 p.Met224Ile missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155000 p.Pro371Leu missense_variant 0.12
katG 2155013 p.Pro367Thr missense_variant 0.11
katG 2155741 p.Gly124Val missense_variant 0.25
katG 2155771 p.Arg114His missense_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170103 c.510C>A synonymous_variant 0.2
PPE35 2170130 c.483C>A synonymous_variant 0.12
PPE35 2170418 p.Met65Ile missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518594 c.480C>A synonymous_variant 0.11
kasA 2518606 c.492G>A synonymous_variant 0.14
kasA 2518757 p.Ala215Ser missense_variant 0.11
kasA 2519165 p.Gly351Cys missense_variant 0.15
eis 2714899 p.Arg145His missense_variant 0.11
eis 2715000 c.333C>A synonymous_variant 0.13
eis 2715057 p.Arg92Gln missense_variant 0.14
folC 2746350 p.Leu417Met missense_variant 0.29
folC 2746576 c.1023C>T synonymous_variant 0.11
folC 2746586 p.Arg338Leu missense_variant 0.19
folC 2746596 p.Ser335Gly missense_variant 0.15
folC 2746597 c.1002C>T synonymous_variant 0.27
folC 2746636 c.963C>A synonymous_variant 0.18
folC 2747336 p.Ala88Glu missense_variant 0.11
folC 2747720 c.-122A>T upstream_gene_variant 0.11
folC 2747784 c.-186C>T upstream_gene_variant 0.2
pepQ 2859592 p.Ala276Val missense_variant 0.12
pepQ 2859961 p.Ala153Glu missense_variant 0.13
pepQ 2859965 p.Ala152Thr missense_variant 0.11
pepQ 2860146 c.273C>T synonymous_variant 0.15
pepQ 2860221 c.198G>A synonymous_variant 0.15
pepQ 2860589 c.-171G>T upstream_gene_variant 0.67
ribD 2986646 c.-193G>T upstream_gene_variant 0.11
ribD 2987333 p.Cys165* stop_gained 0.17
Rv2752c 3066327 c.-136G>A upstream_gene_variant 0.12
Rv2752c 3067037 c.-846G>A upstream_gene_variant 0.12
thyX 3067274 c.672C>A synonymous_variant 0.14
thyX 3067854 p.Gly31Val missense_variant 0.14
thyX 3067991 c.-46G>A upstream_gene_variant 0.13
thyX 3068014 c.-69G>T upstream_gene_variant 0.13
thyX 3068022 c.-77C>A upstream_gene_variant 0.1
thyA 3074522 c.-51C>T upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339047 c.-71G>A upstream_gene_variant 0.11
fbiD 3339052 c.-66G>T upstream_gene_variant 0.11
fbiD 3339339 c.222G>T synonymous_variant 0.14
fbiD 3339347 p.Ala77Val missense_variant 0.11
fbiD 3339743 p.Arg209Leu missense_variant 0.25
fbiD 3339761 c.644G>T stop_lost&splice_region_variant 0.11
Rv3083 3448669 p.Asp56Asn missense_variant 1.0
Rv3083 3448975 c.472C>A synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475302 c.1296C>A synonymous_variant 0.12
Rv3236c 3612167 p.Gly317Val missense_variant 0.15
Rv3236c 3612169 p.Glu316Asp missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
fbiB 3641646 p.Pro38Ser missense_variant 0.15
fbiB 3641908 p.Pro125His missense_variant 0.17
fbiB 3642394 p.Pro287Leu missense_variant 0.21
fbiB 3642667 p.Gly378Val missense_variant 0.22
clpC1 4038186 p.Ala840Val missense_variant 0.15
clpC1 4038223 p.Ala828Thr missense_variant 0.14
clpC1 4040228 c.477G>T synonymous_variant 0.12
clpC1 4040288 c.417C>A synonymous_variant 0.14
clpC1 4040312 c.393G>A synonymous_variant 0.12
embC 4240400 p.Pro180Thr missense_variant 0.11
embC 4240522 c.660C>A synonymous_variant 0.12
embC 4241177 p.Gly439Arg missense_variant 0.11
embC 4241680 c.1818C>A synonymous_variant 0.2
embC 4241693 p.Ala611Ser missense_variant 0.18
embC 4241696 p.Ala612Ser missense_variant 0.11
embC 4242166 c.2304G>A synonymous_variant 0.1
embC 4242172 c.2310C>A synonymous_variant 0.16
embC 4242177 p.Pro772Leu missense_variant 0.11
embA 4242346 c.-887C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243889 c.657G>A synonymous_variant 0.17
embA 4243959 p.Arg243Cys missense_variant 0.12
embA 4244305 p.Arg358Leu missense_variant 0.15
embA 4244430 p.Ile400Leu missense_variant 0.12
embA 4244453 c.1221G>A synonymous_variant 0.15
embA 4245488 c.2256G>T synonymous_variant 0.1
embA 4245660 p.Ala810Thr missense_variant 0.14
embA 4246013 p.Phe927Leu missense_variant 0.11
embB 4246022 c.-492C>T upstream_gene_variant 0.13
embA 4246024 p.Trp931Leu missense_variant 0.11
embB 4246654 c.141G>A synonymous_variant 0.14
embB 4246798 c.285C>T synonymous_variant 0.16
embB 4247005 c.492C>A synonymous_variant 0.11
embB 4247624 p.Pro371Thr missense_variant 0.12
embB 4247641 c.1128G>T synonymous_variant 0.22
embB 4247645 p.Glu378* stop_gained 0.14
embB 4247803 c.1290G>A synonymous_variant 0.18
embB 4249333 c.2820C>A synonymous_variant 0.12
embB 4249367 p.Asp952Tyr missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267676 c.1161G>A synonymous_variant 0.12
aftB 4267967 c.870G>A synonymous_variant 0.19
aftB 4268351 c.486G>A synonymous_variant 0.12
aftB 4268886 c.-50G>A upstream_gene_variant 0.18
aftB 4268891 c.-55G>A upstream_gene_variant 0.18
aftB 4269723 c.-887G>A upstream_gene_variant 0.12
aftB 4269735 c.-899G>A upstream_gene_variant 0.11
ethA 4328023 c.-550G>T upstream_gene_variant 0.11
ethA 4328434 c.-961C>T upstream_gene_variant 0.14
whiB6 4338224 p.Glu100* stop_gained 0.27
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