TB-Profiler result

Run: SRR2101443
Summary

Run ID: SRR2101443

Sample name:

Date: 03-04-2023 23:43:15

Number of reads: 387131

Percentage reads mapped: 99.35

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
ahpC 2726141 c.-52C>T upstream_gene_variant 0.15 isoniazid
embB 4247730 p.Gly406Asp missense_variant 0.25 ethambutol
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 5298 p.Leu20Pro missense_variant 0.1
gyrB 6446 p.Ala403Thr missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7914 p.Leu205Met missense_variant 0.14
gyrA 8694 p.Leu465Met missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.31
rpoB 759866 c.60T>C synonymous_variant 0.14
rpoB 759919 p.Leu38Pro missense_variant 0.12
rpoB 761148 p.Arg448* stop_gained 0.12
rpoB 762024 p.Val740Leu missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763096 p.Tyr1097Phe missense_variant 0.1
rpoB 763219 p.Ala1138Val missense_variant 0.11
rpoC 763904 p.Ala179Ser missense_variant 0.14
rpoC 764127 p.Thr253Asn missense_variant 0.12
rpoC 765077 p.Ser570Pro missense_variant 0.11
rpoC 766500 p.Ala1044Val missense_variant 1.0
rpoC 766563 p.Thr1065Ile missense_variant 0.2
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 777697 p.Ala262Thr missense_variant 0.29
mmpR5 779472 c.485delG frameshift_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302845 c.-86T>A upstream_gene_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1460955 c.-90T>C upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476144 n.2491delG non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
rpsA 1833625 c.84A>G synonymous_variant 0.13
rpsA 1833749 p.Ile70Leu missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101667 p.Ala459Asp missense_variant 0.17
ndh 2101804 c.1239T>C synonymous_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518074 c.-41G>T upstream_gene_variant 0.18
kasA 2518209 p.Thr32Met missense_variant 0.18
kasA 2518525 c.411G>T synonymous_variant 0.11
kasA 2518581 p.Leu156Pro missense_variant 0.15
eis 2714526 c.805_806delAC frameshift_variant 1.0
ahpC 2726223 p.Pro11Ser missense_variant 0.14
ahpC 2726341 p.Val50Gly missense_variant 0.23
folC 2746668 p.Ala311Thr missense_variant 0.25
folC 2747213 p.Pro129Gln missense_variant 0.17
pepQ 2859698 p.Lys241Glu missense_variant 0.22
pepQ 2859755 p.Phe222Ile missense_variant 0.17
pepQ 2860003 p.Glu139Val missense_variant 0.12
ribD 2987188 p.Leu117Gln missense_variant 0.11
ribD 2987390 c.552T>C synonymous_variant 0.2
Rv2752c 3065711 p.Gly161Ser missense_variant 1.0
Rv2752c 3065946 c.246G>T synonymous_variant 0.17
Rv2752c 3067141 c.-950A>G upstream_gene_variant 0.12
thyX 3067350 p.Arg199Leu missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448787 p.Asp95Gly missense_variant 0.12
Rv3083 3449207 p.Pro235Gln missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474818 p.Phe271Ser missense_variant 0.22
fprA 3474935 p.Arg310His missense_variant 0.15
Rv3236c 3612335 p.Met261Lys missense_variant 0.1
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641993 c.459A>G synonymous_variant 0.15
ddn 3987012 p.Gly57Ser missense_variant 0.22
clpC1 4038396 c.2308delG frameshift_variant 0.13
embC 4239729 c.-134G>A upstream_gene_variant 0.18
embC 4240811 p.Phe317Leu missense_variant 0.15
embC 4242542 p.Arg894Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244194 p.Gly321Val missense_variant 0.4
embA 4245925 p.Val898Ala missense_variant 0.22
embA 4246092 p.Phe954Leu missense_variant 0.25
embA 4246446 p.Ala1072Pro missense_variant 0.15
embB 4246701 p.Gln63Arg missense_variant 0.12
embB 4249371 p.Leu953Pro missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269657 c.176delT frameshift_variant 0.11
ethA 4326072 p.Ile468Val missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407923 c.280C>T synonymous_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 1.0