TB-Profiler result

Run: SRR21277516

Summary

Run ID: SRR21277516

Sample name:

Date: 04-04-2023 01:19:36

Number of reads: 13465300

Percentage reads mapped: 97.61

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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490682 c.-101C>A upstream_gene_variant 0.11
fgd1 490960 p.Ala60Thr missense_variant 1.0
fgd1 491318 p.Pro179Gln missense_variant 0.11
fgd1 491323 p.Val181Leu missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575273 c.-75G>A upstream_gene_variant 0.1
mshA 575283 c.-65C>A upstream_gene_variant 0.2
mshA 575421 p.Thr25Asn missense_variant 0.17
mshA 575505 p.His53Leu missense_variant 0.11
mshA 575827 c.480G>A synonymous_variant 0.14
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575916 p.Asp190Val missense_variant 0.19
mshA 576218 p.Pro291Thr missense_variant 0.1
mshA 576232 c.885C>A synonymous_variant 0.12
mshA 576240 p.Ala298Val missense_variant 0.12
mshA 576461 p.Ala372Thr missense_variant 0.5
ccsA 619705 c.-186G>A upstream_gene_variant 0.14
ccsA 619818 c.-73G>T upstream_gene_variant 0.22
ccsA 619948 p.Ser20Thr missense_variant 0.12
ccsA 620187 c.297C>T synonymous_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762691 p.Pro962Gln missense_variant 0.25
rpoC 762791 c.-579G>T upstream_gene_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763925 p.Ala186Thr missense_variant 0.14
rpoC 766094 p.Thr909Ser missense_variant 0.11
rpoC 766967 p.Pro1200Thr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 0.98
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777310 p.Gly391Cys missense_variant 0.22
mmpL5 777357 p.Arg375Leu missense_variant 0.5
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
fbiC 1303102 p.Leu58Met missense_variant 0.12
fbiC 1303954 p.Glu342* stop_gained 0.25
fbiC 1304261 p.Trp444Leu missense_variant 0.13
fbiC 1304432 p.Ser501* stop_gained 0.18
fbiC 1305452 p.Gly841Asp missense_variant 0.13
fbiC 1305455 p.Arg842His missense_variant 0.17
Rv1258c 1406171 c.1170C>T synonymous_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406985 p.Ala119Val missense_variant 0.14
Rv1258c 1407165 p.Thr59Lys missense_variant 0.33
Rv1258c 1407188 c.153C>A synonymous_variant 0.12
Rv1258c 1407518 c.-178C>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834865 p.Gly442Arg missense_variant 0.16
rpsA 1834877 p.Asp446Tyr missense_variant 0.13
tlyA 1917971 p.Leu11Gln missense_variant 0.22
tlyA 1918188 c.249C>T synonymous_variant 0.29
tlyA 1918211 p.Ala91Val missense_variant 0.13
tlyA 1918572 c.633C>A synonymous_variant 0.19
tlyA 1918574 p.Ala212Glu missense_variant 0.38
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155744 p.Gly123Val missense_variant 0.33
katG 2155770 c.342C>A synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169802 p.Asn271Asp missense_variant 1.0
PPE35 2170046 c.567C>T synonymous_variant 0.15
PPE35 2170109 p.Phe168Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518612 c.498C>A synonymous_variant 0.12
kasA 2518656 p.Ala181Glu missense_variant 0.14
kasA 2519020 c.906G>A synonymous_variant 0.21
kasA 2519161 c.1047G>T synonymous_variant 0.18
eis 2714870 p.Gly155Ser missense_variant 0.13
eis 2714883 p.His150Gln missense_variant 0.12
eis 2715024 p.Glu103Asp missense_variant 0.2
eis 2715045 p.Leu96* stop_gained 0.18
eis 2715568 c.-236G>T upstream_gene_variant 0.11
folC 2746307 p.Arg431Leu missense_variant 0.13
folC 2746312 c.1287G>T synonymous_variant 0.14
folC 2746342 c.1257G>A synonymous_variant 0.5
folC 2746349 p.Leu417Arg missense_variant 0.25
folC 2746636 c.963C>A synonymous_variant 0.17
pepQ 2859604 p.Gly272Val missense_variant 0.11
pepQ 2859608 c.811C>A synonymous_variant 0.17
pepQ 2859618 c.801T>A synonymous_variant 0.13
pepQ 2859944 p.Ala159Thr missense_variant 0.18
pepQ 2859947 p.Val158Met missense_variant 0.12
pepQ 2860119 c.300C>T synonymous_variant 0.1
pepQ 2860226 p.Ala65Thr missense_variant 0.1
pepQ 2860584 c.-167_-166delGCinsTT upstream_gene_variant 0.13
ribD 2987305 p.Leu156His missense_variant 0.11
ribD 2987352 p.Thr172Ser missense_variant 0.15
Rv2752c 3066292 c.-101A>T upstream_gene_variant 0.12
Rv2752c 3066302 c.-111C>A upstream_gene_variant 0.13
Rv2752c 3066305 c.-114C>A upstream_gene_variant 0.11
thyX 3067205 c.741G>T synonymous_variant 0.11
thyX 3067216 p.Ser244Cys missense_variant 0.11
thyX 3067217 c.729C>T synonymous_variant 0.25
thyX 3067248 p.Thr233Ile missense_variant 0.43
thyX 3067307 c.639C>A synonymous_variant 0.17
thyX 3067547 c.399C>A synonymous_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087335 c.516G>T synonymous_variant 0.12
fbiD 3338962 c.-156G>T upstream_gene_variant 0.14
fbiD 3339307 p.Pro64Asn missense_variant 0.14
fbiD 3339320 p.Ala68Glu missense_variant 0.18
fbiD 3339337 p.Gly74Trp missense_variant 0.11
fbiD 3339556 p.Gly147Arg missense_variant 0.12
fbiD 3339734 p.Ala206Val missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474926 p.Thr307Asn missense_variant 0.14
fprA 3474928 p.Gly308Lys missense_variant 0.12
fprA 3474988 p.Pro328Ser missense_variant 0.2
fprA 3475309 p.Glu435* stop_gained 0.18
fprA 3475314 c.1308G>T synonymous_variant 0.23
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
fbiB 3641626 p.Ala31Asp missense_variant 0.1
fbiB 3641641 p.Ala36Val missense_variant 0.11
fbiB 3641927 c.393C>A synonymous_variant 0.25
fbiB 3642004 p.Arg157Leu missense_variant 0.14
fbiB 3642011 c.477C>T synonymous_variant 0.11
fbiB 3642177 p.Ala215Thr missense_variant 0.1
fbiB 3642214 p.Ser227* stop_gained 0.18
fbiB 3642220 p.Ala229Asp missense_variant 0.22
fbiB 3642242 c.708C>T synonymous_variant 0.18
fbiB 3642367 p.Ala278Asp missense_variant 0.17
fbiB 3642375 p.Ala281Thr missense_variant 0.29
alr 3841207 p.His72Asn missense_variant 0.12
clpC1 4038186 p.Ala840Val missense_variant 0.27
panD 4044475 c.-194G>T upstream_gene_variant 0.14
embC 4240642 c.780G>T synonymous_variant 0.12
embC 4241686 c.1824G>A synonymous_variant 0.11
embC 4242167 p.Val769Met missense_variant 0.11
embC 4242366 p.Ser835Tyr missense_variant 0.22
embC 4242368 p.Arg836Ser missense_variant 0.12
embC 4242375 p.Arg838Gln missense_variant 0.43
embC 4242711 p.Gln950Leu missense_variant 0.17
embA 4242724 c.-509G>T upstream_gene_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243483 p.Ala84Asp missense_variant 0.11
embA 4243882 p.Ala217Asp missense_variant 0.11
embA 4243892 c.660G>A synonymous_variant 0.13
embA 4243960 p.Arg243Leu missense_variant 0.12
embA 4244211 p.Pro327Thr missense_variant 0.12
embA 4244221 p.Leu330Gln missense_variant 0.29
embA 4244303 c.1071C>T synonymous_variant 0.14
embA 4244306 c.1074G>T synonymous_variant 0.1
embA 4244438 c.1206C>A synonymous_variant 0.11
embA 4244444 c.1212G>A synonymous_variant 0.17
embA 4244446 p.Leu405Gln missense_variant 0.25
embA 4244574 p.Ala448Ser missense_variant 0.25
embA 4244856 p.Ala542Thr missense_variant 0.12
embA 4245447 p.Val739Met missense_variant 0.13
embA 4245458 p.Glu742Asp missense_variant 0.15
embA 4245467 c.2235C>T synonymous_variant 0.11
embB 4246798 c.285C>T synonymous_variant 0.27
embB 4246799 p.Gly96Cys missense_variant 0.17
embB 4247015 p.Ser168Thr missense_variant 0.11
embB 4247022 p.Ala170Glu missense_variant 0.15
embB 4247625 p.Pro371His missense_variant 0.3
embB 4247648 p.Ala379Ser missense_variant 0.18
embB 4247855 p.Gly448Ser missense_variant 0.27
embB 4247860 c.1347G>A synonymous_variant 1.0
embB 4247911 c.1398G>A synonymous_variant 0.2
embB 4248590 p.Ala693Asn missense_variant 0.13
embB 4248594 p.Gly694Asp missense_variant 0.5
embB 4248598 p.Glu695Asp missense_variant 0.6
embB 4248599 p.Gly696Trp missense_variant 0.2
embB 4248621 p.Thr703Met missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267948 p.Asp297Tyr missense_variant 0.13
aftB 4267950 p.Pro296His missense_variant 0.11
aftB 4268251 p.Ala196Ser missense_variant 0.12
aftB 4268282 c.555G>A synonymous_variant 0.14
aftB 4268291 p.Ser182Arg missense_variant 0.12
ethR 4328035 p.Pro163Thr missense_variant 0.12
ethA 4328043 c.-570G>A upstream_gene_variant 0.12
ethA 4328432 c.-959A>T upstream_gene_variant 0.12
whiB6 4338323 p.Val67Ile missense_variant 0.18
whiB6 4338331 p.Arg64His missense_variant 0.11
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