TB-Profiler result

Run: SRR6789629
Summary

Run ID: SRR6789629

Sample name:

Date: 04-04-2023 16:04:21

Number of reads: 1310770

Percentage reads mapped: 98.0

Strain: lineage2.2.1;lineage1.1.2

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 0.66
lineage1 Indo-Oceanic EAI RD239 0.3
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.38
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.62
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.34
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.7
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
gyrB 6112 p.Met291Ile missense_variant 0.51
gyrB 6124 c.885C>T synonymous_variant 0.48
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.31
gyrA 9143 c.1842T>C synonymous_variant 0.31
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.6
ccsA 620051 p.Val54Glu missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 0.75
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.27
rpoC 763886 c.517C>A synonymous_variant 0.34
rpoC 765171 p.Pro601Leu missense_variant 0.27
rpoC 765787 c.2418C>T synonymous_variant 0.56
rpoC 766765 c.3396A>C synonymous_variant 0.13
rpoC 766774 c.3405T>C synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.71
mmpR5 779158 p.Ala57Ser missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.77
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303757 p.Ala276Glu missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.62
embR 1417019 p.Cys110Tyr missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
fabG1 1673890 p.Ala151Ser missense_variant 0.19
inhA 1673988 c.-214G>A upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.64
rpsA 1834411 c.870T>C synonymous_variant 0.15
rpsA 1834417 c.876G>C synonymous_variant 0.13
rpsA 1834423 c.882G>C synonymous_variant 0.12
rpsA 1834435 c.894G>C synonymous_variant 0.14
rpsA 1834451 c.910T>C synonymous_variant 0.14
rpsA 1834465 c.924T>C synonymous_variant 0.16
rpsA 1834468 c.927A>G synonymous_variant 0.15
rpsA 1834528 c.987T>C synonymous_variant 0.1
rpsA 1834609 c.1068T>C synonymous_variant 0.15
rpsA 1834618 c.1077G>C synonymous_variant 0.13
rpsA 1834633 c.1092A>G synonymous_variant 0.14
rpsA 1834639 c.1098T>C synonymous_variant 0.14
rpsA 1834654 p.Glu371Asp missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.38
PPE35 2170048 p.Leu189Val missense_variant 0.37
PPE35 2170053 p.Thr187Ser missense_variant 0.38
Rv1979c 2222308 p.Asp286Gly missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.25
kasA 2518927 c.813C>A synonymous_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 0.21
Rv2752c 3064632 c.1560C>T synonymous_variant 0.17
Rv2752c 3066350 c.-159T>A upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086789 c.-31A>G upstream_gene_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.57
fprA 3475159 p.Asn385Asp missense_variant 0.38
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77
Rv3236c 3612988 c.129A>G synonymous_variant 0.3
fbiB 3642272 c.738C>T synonymous_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.29
embC 4241042 p.Asn394Asp missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.75
embA 4243848 p.Val206Met missense_variant 0.31
embA 4244911 p.Leu560Pro missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 0.46
embB 4246555 c.42G>C synonymous_variant 0.11
embB 4247646 p.Glu378Ala missense_variant 0.34
aftB 4267647 p.Asp397Gly missense_variant 0.64
aftB 4269006 c.-170T>C upstream_gene_variant 0.12
aftB 4269012 c.-176G>C upstream_gene_variant 0.14
aftB 4269027 c.-191C>T upstream_gene_variant 0.16
aftB 4269033 c.-197T>C upstream_gene_variant 0.15
aftB 4269036 c.-200C>G upstream_gene_variant 0.14
aftB 4269042 c.-206G>C upstream_gene_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 0.32
aftB 4269606 c.-770T>C upstream_gene_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.31
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.52
gid 4407873 c.330G>T synonymous_variant 0.4
gid 4407927 p.Glu92Asp missense_variant 0.6