TB-Profiler result

Run: SRR21277812

Summary

Run ID: SRR21277812

Sample name:

Date: 04-04-2023 01:45:08

Number of reads: 13715838

Percentage reads mapped: 97.53

Strain: lineage2.2.1

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
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575414 p.Gly23Ser missense_variant 0.12
mshA 575423 p.Arg26Ser missense_variant 0.12
mshA 575454 p.Arg36Pro missense_variant 0.11
mshA 575500 c.153G>T synonymous_variant 0.13
mshA 575870 p.His175Asn missense_variant 0.14
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575915 p.Asp190Tyr missense_variant 0.12
mshA 576223 c.876G>T synonymous_variant 0.11
mshA 576450 p.Pro368Gln missense_variant 0.11
mshA 576457 c.1110G>A synonymous_variant 0.17
ccsA 619983 c.93G>A synonymous_variant 0.12
ccsA 619984 p.Leu32Met missense_variant 0.17
ccsA 620148 c.258G>T synonymous_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763919 p.Leu184Met missense_variant 0.12
rpoC 763933 c.564C>A synonymous_variant 0.25
rpoC 763955 p.Lys196* stop_gained 0.15
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 777290 c.1191G>T synonymous_variant 0.11
mmpL5 777299 c.1182G>T synonymous_variant 0.12
mmpL5 777330 p.Ala384Asp missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801236 p.Ala143Glu missense_variant 0.11
rplC 801254 p.Gly149Val missense_variant 0.12
fbiC 1303109 p.Ala60Glu missense_variant 0.19
fbiC 1303127 p.Arg66Leu missense_variant 0.27
fbiC 1303930 p.Pro334Thr missense_variant 0.2
fbiC 1304188 p.Pro420Thr missense_variant 0.33
fbiC 1304262 p.Trp444Cys missense_variant 0.13
fbiC 1304265 c.1335C>T synonymous_variant 0.15
fbiC 1304440 p.Arg504Ser missense_variant 0.11
fbiC 1304452 p.Gly508Cys missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99
Rv1258c 1406986 p.Ala119Ser missense_variant 0.15
Rv1258c 1407098 p.Leu81Ile missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673573 p.Thr45Ile missense_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.95
tlyA 1918064 p.Pro42Leu missense_variant 0.1
tlyA 1918182 c.243G>A synonymous_variant 0.18
tlyA 1918208 p.Gly90Val missense_variant 0.16
tlyA 1918566 c.627C>A synonymous_variant 0.16
tlyA 1918580 p.Arg214Leu missense_variant 0.19
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155743 p.Gly123Val missense_variant 0.13
katG 2155755 c.357C>A synonymous_variant 0.33
katG 2155758 c.354C>A synonymous_variant 0.17
katG 2155766 p.His116Asn missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170091 c.522T>A synonymous_variant 0.33
PPE35 2170105 p.Leu170Ile missense_variant 0.11
PPE35 2170354 p.Ala87Ser missense_variant 0.12
PPE35 2170355 c.258G>T synonymous_variant 0.15
PPE35 2170418 p.Met65Ile missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519067 p.Gly318Asp missense_variant 0.15
kasA 2519157 p.Gly348Val missense_variant 0.14
eis 2715036 c.297G>T synonymous_variant 0.16
eis 2715054 c.279G>A synonymous_variant 0.16
folC 2746313 p.Arg429Leu missense_variant 0.11
folC 2746332 p.Glu423* stop_gained 0.22
folC 2746350 p.Leu417Met missense_variant 0.25
folC 2746351 c.1248C>A synonymous_variant 0.15
folC 2746586 p.Arg338Leu missense_variant 0.1
folC 2746632 p.Gly323Ser missense_variant 0.11
pepQ 2859600 c.819G>T synonymous_variant 0.11
pepQ 2859605 p.Gly272Trp missense_variant 0.33
pepQ 2859935 p.Gly162Cys missense_variant 0.12
pepQ 2859941 p.Arg160Ser missense_variant 0.11
pepQ 2860147 p.Gly91Val missense_variant 0.14
pepQ 2860227 c.192C>A synonymous_variant 0.11
pepQ 2860580 c.-162G>T upstream_gene_variant 0.12
pepQ 2860583 c.-165G>T upstream_gene_variant 0.12
pepQ 2860589 c.-171G>T upstream_gene_variant 0.78
ribD 2986650 c.-189G>T upstream_gene_variant 0.1
ribD 2987308 p.Ala157Glu missense_variant 0.12
thyX 3067247 c.699C>A synonymous_variant 0.15
thyX 3067289 c.657C>A synonymous_variant 0.15
thyX 3067300 p.Leu216Met missense_variant 0.15
thyX 3067431 p.Arg172His missense_variant 0.14
thyX 3067542 p.Ala135Asp missense_variant 0.11
thyX 3067547 c.399C>A synonymous_variant 0.12
thyX 3067874 c.72C>T synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087325 p.Ala169Asp missense_variant 0.17
fbiD 3339306 c.189C>A synonymous_variant 0.11
fbiD 3339328 p.Ala71Thr missense_variant 0.15
fbiD 3339339 c.222G>T synonymous_variant 0.18
fbiD 3339689 p.Thr191Ile missense_variant 0.4
fbiD 3339737 p.Thr207Ile missense_variant 0.21
fbiD 3339746 p.Ala210Val missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474927 c.921C>A synonymous_variant 0.14
fprA 3474930 c.924C>A synonymous_variant 0.12
fprA 3474982 p.Gly326Trp missense_variant 0.12
fprA 3475301 p.Ala432Asp missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642221 c.687C>T synonymous_variant 0.18
fbiB 3642353 c.819C>A synonymous_variant 0.11
alr 3840639 p.Ser261Asn missense_variant 1.0
alr 3841129 p.Leu98Val missense_variant 0.25
alr 3841197 p.Thr75Lys missense_variant 0.1
alr 3841200 p.Ala74Asp missense_variant 0.13
embC 4240472 p.Leu204Met missense_variant 0.11
embC 4240484 p.Ala208Ser missense_variant 0.11
embC 4240604 p.Leu248Met missense_variant 0.13
embC 4242368 p.Arg836Ser missense_variant 0.1
embC 4242479 p.Thr873Ser missense_variant 0.29
embC 4242581 p.Ala907Thr missense_variant 0.13
embA 4242631 c.-602G>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243479 p.Pro83Thr missense_variant 0.11
embA 4243511 c.279G>T synonymous_variant 0.13
embA 4243618 p.Ser129Phe missense_variant 0.1
embA 4243904 c.672G>A synonymous_variant 0.11
embA 4243922 c.690C>T synonymous_variant 0.12
embA 4244499 p.Pro423Thr missense_variant 0.27
embA 4244522 c.1290C>A synonymous_variant 0.5
embA 4244574 p.Ala448Ser missense_variant 0.4
embA 4244588 c.1356G>T synonymous_variant 0.17
embB 4246669 c.156C>A synonymous_variant 0.12
embB 4246795 c.282G>T synonymous_variant 0.11
embB 4247627 p.Arg372Ser missense_variant 0.1
embB 4247641 c.1128G>T synonymous_variant 0.22
embB 4247647 p.Glu378Asp missense_variant 0.12
embB 4247865 p.Ala451Glu missense_variant 0.2
embB 4247904 p.Arg464Leu missense_variant 0.11
embB 4248583 c.2070C>A synonymous_variant 0.16
embB 4248596 p.Glu695* stop_gained 0.12
embB 4248601 c.2088G>T synonymous_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267671 p.Ala389Glu missense_variant 0.16
aftB 4267925 c.912G>T synonymous_variant 0.13
aftB 4267929 p.Arg303Leu missense_variant 0.11
aftB 4267931 c.906C>T synonymous_variant 0.12
ethA 4328460 c.-987G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 1.0