TB-Profiler result

Run: SRR12199477
Summary

Run ID: SRR12199477

Sample name:

Date: 03-04-2023 06:42:41

Number of reads: 481424

Percentage reads mapped: 87.99

Strain: lineage1.1.1

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
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.98
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.96
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 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.85
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766977 p.Gly1203Val missense_variant 0.4
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777146 c.1335C>T synonymous_variant 0.47
mmpL5 777251 c.1230C>T synonymous_variant 0.32
mmpS5 778799 p.Gly36Ala missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155098 c.1014C>T synonymous_variant 0.71
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2222012 p.Gln385* stop_gained 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223144 p.Arg7Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289987 c.-746C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.88
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.88
fprA 3475159 p.Asn385Asp missense_variant 0.79
Rv3236c 3612926 p.Ile64Ser missense_variant 0.33
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4043882 p.Pro134Ser missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247239 c.726G>A synonymous_variant 0.93
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248359 p.Pro616Thr missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.15
aftB 4267873 p.Gln322Glu missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 0.94
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408286 c.-84C>T upstream_gene_variant 0.75