TB-Profiler result

Run: SRR21277770
Summary

Run ID: SRR21277770

Sample name:

Date: 04-04-2023 01:40:39

Number of reads: 14535144

Percentage reads mapped: 98.09

Strain: lineage2.2.1.1

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 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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
gid 4407967 p.Leu79Ser 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
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 491295 c.513C>A synonymous_variant 0.11
fgd1 491311 p.Gly177Arg missense_variant 0.12
fgd1 491321 p.Ala180Val missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575494 c.147G>T synonymous_variant 0.15
mshA 575499 p.Ala51Val missense_variant 0.15
mshA 575870 p.His175Asn missense_variant 0.29
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576457 c.1110G>A synonymous_variant 0.17
mshA 576602 c.1255C>A synonymous_variant 0.5
ccsA 620135 p.Ala82Val missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 762776 c.-594C>T upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763933 c.564C>A synonymous_variant 0.14
rpoC 764579 p.Asp404Tyr missense_variant 0.14
rpoC 766048 c.2679C>A synonymous_variant 0.11
rpoC 766106 p.Asp913Tyr missense_variant 0.12
rpoC 766969 c.3600C>A synonymous_variant 0.15
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 779355 c.-875C>A upstream_gene_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801245 p.Arg146His missense_variant 0.19
rplC 801252 c.444G>T synonymous_variant 0.11
fbiC 1303104 c.174G>A synonymous_variant 0.12
fbiC 1303107 p.Cys59* stop_gained 0.11
fbiC 1303114 p.Ala62Thr missense_variant 0.2
fbiC 1303935 c.1005G>T synonymous_variant 0.13
fbiC 1304261 p.Trp444Leu missense_variant 0.1
fbiC 1305452 p.Gly841Asp missense_variant 0.19
fbiC 1305456 c.2526C>A synonymous_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406964 p.Ser126Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834869 p.Arg443His missense_variant 0.12
tlyA 1917955 p.Arg6Ser missense_variant 0.17
tlyA 1917970 p.Leu11Met missense_variant 0.22
tlyA 1918059 c.120C>T synonymous_variant 0.12
tlyA 1918176 c.237C>A synonymous_variant 0.15
tlyA 1918191 c.252G>T synonymous_variant 0.17
tlyA 1918252 p.Ala105Ser missense_variant 0.11
tlyA 1918566 c.627C>A synonymous_variant 0.27
tlyA 1918588 p.Glu217* stop_gained 0.19
tlyA 1918602 c.663C>T synonymous_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155757 p.Arg119Ser missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168788 p.Thr609Ala missense_variant 0.38
PPE35 2170037 c.576C>T synonymous_variant 0.23
PPE35 2170103 c.510C>A synonymous_variant 0.11
PPE35 2170446 p.Ser56* stop_gained 0.11
Rv1979c 2223062 p.Thr35Ala missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519047 p.His311Gln missense_variant 0.14
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2715045 c.288G>A synonymous_variant 0.67
folC 2746342 c.1257G>A synonymous_variant 0.14
folC 2746347 p.Ala418Thr missense_variant 0.13
folC 2746577 p.Arg341Leu missense_variant 0.11
folC 2747715 c.-117G>T upstream_gene_variant 0.11
pepQ 2859600 c.819G>T synonymous_variant 0.11
pepQ 2859603 p.Gly272Cys missense_variant 0.1
pepQ 2859610 p.Leu270Gln missense_variant 0.11
pepQ 2859919 p.Arg167Leu missense_variant 0.13
pepQ 2859941 p.Arg160Ser missense_variant 0.25
pepQ 2859954 c.465C>A synonymous_variant 0.15
pepQ 2860583 c.-165G>T upstream_gene_variant 0.14
pepQ 2860589 c.-171G>T upstream_gene_variant 0.64
ribD 2986647 c.-192G>T upstream_gene_variant 0.11
ribD 2987306 c.468C>A synonymous_variant 0.2
Rv2752c 3066297 c.-106G>A upstream_gene_variant 0.11
thyX 3067300 p.Leu216Met missense_variant 0.18
thyX 3067302 p.Cys215Phe missense_variant 0.1
thyX 3067541 p.Ala135Glu missense_variant 0.2
thyX 3067856 c.90C>T synonymous_variant 0.12
thyX 3068001 c.-56G>T upstream_gene_variant 0.13
thyA 3074198 p.Pro92Ser missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087296 c.477G>A synonymous_variant 0.12
fbiD 3339319 p.Ala68Thr missense_variant 0.11
fbiD 3339339 c.222G>T synonymous_variant 0.21
fbiD 3339436 p.Ala107Thr missense_variant 1.0
fbiD 3339561 c.444C>A synonymous_variant 0.19
fbiD 3339746 p.Ala210Val missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474928 p.Gly308Ser missense_variant 0.12
fprA 3474981 c.975C>T synonymous_variant 0.18
fprA 3474987 c.981G>T synonymous_variant 0.12
fprA 3475309 p.Glu435* stop_gained 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
fbiB 3641625 p.Ala31Thr missense_variant 0.11
fbiB 3641903 c.369C>A synonymous_variant 0.11
fbiB 3642029 c.495C>T synonymous_variant 0.11
fbiB 3642273 p.Glu247* stop_gained 0.17
fbiB 3642382 p.Ala283Val missense_variant 0.11
fbiB 3642394 p.Pro287Leu missense_variant 0.11
alr 3841471 c.-51A>T upstream_gene_variant 0.21
embC 4241253 p.Ser464Phe missense_variant 0.11
embC 4241689 c.1827G>A synonymous_variant 0.19
embC 4242371 p.Ala837Thr missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242725 p.Gln955* stop_gained 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243478 c.246G>A synonymous_variant 0.11
embA 4243616 c.384C>T synonymous_variant 0.17
embA 4243905 p.Asp225Asn missense_variant 0.11
embA 4243947 p.Arg239* stop_gained 0.11
embA 4244210 c.978G>A synonymous_variant 0.13
embA 4244213 c.981C>A synonymous_variant 0.12
embA 4244438 c.1206C>A synonymous_variant 0.17
embA 4244443 p.Arg404Gln missense_variant 0.11
embA 4244446 p.Leu405Gln missense_variant 0.17
embA 4244597 c.1365G>T synonymous_variant 0.21
embA 4244606 c.1374G>T synonymous_variant 0.13
embA 4244848 p.Gly539Asp missense_variant 0.1
embA 4244864 c.1632G>A synonymous_variant 0.14
embA 4245669 p.Ala813Thr missense_variant 0.1
embA 4245772 p.Asn847Ser missense_variant 1.0
embB 4246654 c.141G>A synonymous_variant 0.17
embB 4246688 p.Pro59Thr missense_variant 0.14
embB 4247123 p.Ala204Ser missense_variant 0.12
embB 4247863 c.1350C>A synonymous_variant 0.19
embB 4247869 c.1356G>A synonymous_variant 0.18
embB 4247870 p.Ala453Thr missense_variant 0.29
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248593 p.Gly694Ser missense_variant 0.12
embB 4248597 p.Glu695Val missense_variant 0.12
embB 4248603 p.Arg697Leu missense_variant 0.11
embB 4249119 p.Asp869Gly missense_variant 1.0
aftB 4267622 c.1215G>T synonymous_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 0.91
aftB 4267676 c.1161G>A synonymous_variant 0.11
aftB 4267931 c.906C>T synonymous_variant 0.17
aftB 4267955 c.882G>A synonymous_variant 0.16
aftB 4267969 p.Leu290Met missense_variant 0.12
ubiA 4269714 p.Leu40Phe missense_variant 0.11
ethR 4328032 p.Ala162Thr missense_variant 0.11
ethA 4328037 c.-564C>T upstream_gene_variant 0.11
ethA 4328433 c.-960G>T upstream_gene_variant 0.12
whiB6 4338320 p.Glu68* stop_gained 0.13
whiB6 4338326 p.Ala66Thr missense_variant 0.1
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