TB-Profiler result

Run: SRR6046617
Summary

Run ID: SRR6046617

Sample name:

Date: 04-04-2023 12:20:16

Number of reads: 583828

Percentage reads mapped: 89.54

Strain: lineage2.2.1

Drug-resistance: HR-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
katG 2155018 p.Pro365Leu missense_variant 0.12 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 5810 p.Ala191Ser missense_variant 0.12
gyrB 5879 p.Thr214Ala missense_variant 0.11
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 491485 p.Tyr235Asn missense_variant 0.17
fgd1 491530 p.Ala250Ser missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575878 c.531A>C synonymous_variant 0.14
mshA 575907 p.Ala187Val missense_variant 0.92
mshA 576421 c.1074T>C synonymous_variant 0.1
ccsA 620178 c.288G>C synonymous_variant 0.17
ccsA 620187 c.297C>T synonymous_variant 0.14
ccsA 620197 p.Gln103Thr missense_variant 0.12
ccsA 620202 c.312G>C synonymous_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760235 c.429T>C synonymous_variant 0.14
rpoB 760244 c.438G>C synonymous_variant 0.12
rpoB 760253 c.447T>C synonymous_variant 0.13
rpoB 760274 c.468G>A synonymous_variant 0.12
rpoB 761027 c.1221A>T synonymous_variant 0.12
rpoB 761036 c.1230G>C synonymous_variant 0.12
rpoB 761037 c.1231T>C synonymous_variant 0.12
rpoB 761051 c.1245G>T synonymous_variant 0.13
rpoB 761054 c.1248G>C synonymous_variant 0.13
rpoB 761057 c.1251G>C synonymous_variant 0.14
rpoB 761060 c.1254C>G synonymous_variant 0.14
rpoB 761063 c.1257C>G synonymous_variant 0.14
rpoB 761084 c.1278C>A synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.94
rpoC 766996 c.3627C>T synonymous_variant 0.13
rpoC 767008 c.3639G>A synonymous_variant 0.14
rpoC 767020 c.3651C>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775851 p.Ser877Thr missense_variant 0.12
mmpL5 775857 p.Gly875Ala missense_variant 0.12
mmpL5 775865 c.2616T>C synonymous_variant 0.12
mmpL5 775885 p.Ile866Leu missense_variant 0.1
mmpL5 775886 c.2595A>G synonymous_variant 0.1
mmpL5 775916 c.2565T>C synonymous_variant 0.14
mmpL5 775939 p.Ala848Ser missense_variant 0.14
mmpL5 775951 c.2530C>T synonymous_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778588 p.Gln106His missense_variant 0.38
mmpS5 778780 p.Lys42Asn missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781706 c.147T>G synonymous_variant 0.12
rpsL 781709 c.150G>C synonymous_variant 0.11
rpsL 781715 c.156T>C synonymous_variant 0.11
rpsL 781742 c.183C>T synonymous_variant 0.12
rpsL 781754 c.195G>C synonymous_variant 0.12
rpsL 781802 c.243G>C synonymous_variant 0.11
rpsL 781808 c.249C>T synonymous_variant 0.12
rplC 800681 c.-128C>A upstream_gene_variant 0.12
fbiC 1305435 c.2505G>C synonymous_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416470 p.His293Arg missense_variant 0.12
atpE 1460927 c.-118C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473954 n.297A>G non_coding_transcript_exon_variant 0.17
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.12
rrl 1474603 n.946C>A non_coding_transcript_exon_variant 0.15
rrl 1474616 n.959G>T non_coding_transcript_exon_variant 0.15
rrl 1476201 n.2544C>A non_coding_transcript_exon_variant 0.22
rrl 1476704 n.3053delC non_coding_transcript_exon_variant 0.13
rpsA 1833949 c.408T>C synonymous_variant 0.14
rpsA 1833997 c.456G>C synonymous_variant 0.1
rpsA 1834015 c.474G>C synonymous_variant 0.1
rpsA 1834021 c.480C>T synonymous_variant 0.11
rpsA 1834030 c.489C>G synonymous_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834456 c.915T>G synonymous_variant 0.1
rpsA 1834489 c.948T>C synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154760 p.Gly451Asp missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170205 c.408C>T synonymous_variant 0.33
Rv1979c 2222681 p.Ala162Thr missense_variant 0.2
Rv1979c 2223060 c.105T>C synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289960 c.-719C>A upstream_gene_variant 0.17
kasA 2518477 p.Arg121Ser missense_variant 0.13
kasA 2519143 c.1029G>C synonymous_variant 0.1
kasA 2519183 c.1069_1071delCTCinsTTG synonymous_variant 0.12
kasA 2519188 c.1074G>A synonymous_variant 0.13
kasA 2519194 c.1080G>C synonymous_variant 0.12
kasA 2519195 p.Thr361Ala missense_variant 0.11
kasA 2519209 c.1095C>G synonymous_variant 0.11
kasA 2519218 c.1104G>C synonymous_variant 0.12
kasA 2519224 c.1110C>G synonymous_variant 0.12
kasA 2519239 c.1125A>G synonymous_variant 0.12
kasA 2519242 c.1128C>G synonymous_variant 0.12
kasA 2519329 c.1215C>A synonymous_variant 0.12
eis 2714917 p.Glu139Gly missense_variant 0.12
folC 2746961 p.Ala213Val missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087248 p.Gln143His missense_variant 0.11
fbiD 3339710 p.Ala198Glu missense_variant 0.17
Rv3083 3449224 p.Glu241* stop_gained 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475155 c.1149C>A synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641826 c.292C>A synonymous_variant 0.15
fbiB 3642007 p.Asn158Ser missense_variant 0.17
fbiB 3642746 c.1212C>T synonymous_variant 0.14
rpoA 3878001 c.507A>G synonymous_variant 0.11
clpC1 4040267 c.438A>G synonymous_variant 0.2
clpC1 4040273 c.432T>C synonymous_variant 0.2
clpC1 4040276 c.429C>G synonymous_variant 0.2
clpC1 4040291 c.414G>C synonymous_variant 0.18
clpC1 4040300 c.405C>T synonymous_variant 0.18
clpC1 4040306 c.399G>C synonymous_variant 0.18
clpC1 4040330 c.375C>G synonymous_variant 0.14
clpC1 4040333 c.372G>C synonymous_variant 0.14
clpC1 4040342 c.363C>T synonymous_variant 0.12
clpC1 4040348 c.357G>C synonymous_variant 0.12
clpC1 4040354 c.351A>G synonymous_variant 0.12
clpC1 4040363 c.342A>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244769 p.Gly513Trp missense_variant 0.22
embB 4246559 c.50delT frameshift_variant 0.18
embB 4249757 p.Thr1082Ala missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326268 c.1206C>A synonymous_variant 0.13
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