TB-Profiler result

Run: SRR12199476

Summary

Run ID: SRR12199476

Sample name:

Date: 03-04-2023 06:42:45

Number of reads: 417890

Percentage reads mapped: 46.7

Strain: lineage1.1.3

Drug-resistance: Sensitive


Download CSV Download TXT Download PDF Download JSON
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 0.97
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 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 5477 p.Asp80Tyr missense_variant 0.15
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6436 c.-866C>T upstream_gene_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 0.8
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490685 c.-98G>T upstream_gene_variant 0.9
fgd1 491007 c.225G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_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 0.86
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406388 p.Cys318Phe missense_variant 0.22
embR 1416357 p.Val331Ile missense_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473953 n.296T>A non_coding_transcript_exon_variant 1.0
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 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.42
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.83
ahpC 2726051 c.-142G>A upstream_gene_variant 0.89
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3067549 p.Thr133Pro missense_variant 0.18
ald 3086750 c.-70A>C upstream_gene_variant 0.86
ald 3086788 c.-32T>C upstream_gene_variant 0.9
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.95
alr 3840591 p.Val277Gly missense_variant 0.22
alr 3840689 c.732C>T synonymous_variant 0.43
alr 3841253 c.168C>T synonymous_variant 0.9
alr 3841277 c.144C>T synonymous_variant 0.91
clpC1 4040517 p.Val63Ala missense_variant 0.94
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 4245969 p.Pro913Ser missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.57
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267894 p.Ile315Phe missense_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 0.73
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.6
gid 4407873 c.330G>T synonymous_variant 0.67
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0