TB-Profiler result

Run: ERR2512736
Summary

Run ID: ERR2512736

Sample name:

Date: 31-03-2023 19:13:19

Number of reads: 789189

Percentage reads mapped: 99.57

Strain: lineage4;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 0.95
lineage4 Euro-American LAM;T;S;X;H None 0.06
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.95
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.92
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 7589 c.288G>T synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.93
mshA 575282 c.-66C>T upstream_gene_variant 1.0
mshA 575294 c.-54C>T upstream_gene_variant 0.14
mshA 575314 c.-34C>A upstream_gene_variant 0.13
mshA 575722 c.375G>A synonymous_variant 0.18
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576316 c.969A>G synonymous_variant 0.12
mshA 576616 c.1269G>A synonymous_variant 0.14
ccsA 620186 p.Gly99Ala missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.94
rpoB 760185 c.379C>T synonymous_variant 0.13
rpoB 760982 c.1176G>C synonymous_variant 0.11
rpoB 761862 p.Ala686Thr missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.88
rpoC 763970 p.Gly201Ser missense_variant 0.14
rpoC 764165 p.Glu266Lys missense_variant 0.12
rpoC 766086 p.Pro906Leu missense_variant 0.15
rpoC 766208 p.Pro947Ser missense_variant 0.29
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 777312 p.Pro390Leu missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801042 c.234C>G synonymous_variant 0.1
rplC 801354 c.546G>A synonymous_variant 0.14
fbiC 1302744 c.-187C>T upstream_gene_variant 0.12
fbiC 1303966 c.1036C>T synonymous_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 0.88
embR 1417132 c.216C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472335 n.490A>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>G non_coding_transcript_exon_variant 0.12
inhA 1673451 c.-751A>G upstream_gene_variant 0.11
inhA 1673526 c.-676G>A upstream_gene_variant 0.13
fabG1 1673552 p.Asp38Gly missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102249 p.Thr265Ile missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 0.95
katG 2155970 c.142C>T synonymous_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290069 c.-828C>T upstream_gene_variant 0.12
kasA 2518288 c.174C>T synonymous_variant 0.13
eis 2715010 p.Ile108Thr missense_variant 0.15
folC 2746747 c.852G>A synonymous_variant 0.12
pepQ 2859959 c.460C>T synonymous_variant 0.12
pepQ 2860176 c.243C>T synonymous_variant 0.18
thyX 3067621 p.Val109Ile missense_variant 0.18
thyX 3067968 c.-23C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339459 c.342A>G synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474312 c.306C>T synonymous_variant 0.12
Rv3236c 3612752 p.Ala122Val missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613303 c.-187C>T upstream_gene_variant 0.13
fbiB 3641570 c.36C>A synonymous_variant 0.17
alr 3840983 c.438C>T synonymous_variant 0.12
ddn 3987082 p.Gly80Asp missense_variant 0.15
embC 4240798 c.936C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.92
embA 4243858 p.Leu209His missense_variant 0.14
embB 4246403 c.-111G>A upstream_gene_variant 0.15
embA 4246498 p.Pro1089Leu missense_variant 0.25
embB 4247191 c.678C>A synonymous_variant 0.14
aftB 4267282 p.Glu519Lys missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 0.92
ubiA 4269872 c.-39G>A upstream_gene_variant 0.13
ethA 4328220 c.-747G>T upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.86