TB-Profiler result

Run: SRR12199446
Summary

Run ID: SRR12199446

Sample name:

Date: 03-04-2023 06:40:50

Number of reads: 2535450

Percentage reads mapped: 99.03

Strain: lineage1.1.3.1

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
lineage1 Indo-Oceanic EAI RD239 0.96
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.97
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.93
lineage1.1.3.1 Indo-Oceanic NA RD239 0.94
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
katG 2155168 p.Ser315Thr missense_variant 0.11 isoniazid
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 5121 c.-119A>T upstream_gene_variant 0.5
gyrB 6112 p.Met291Ile missense_variant 0.94
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 0.93
gyrA 9304 p.Gly668Asp missense_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 0.94
rpoC 763886 c.517C>A synonymous_variant 0.94
rpoC 765171 p.Pro601Leu missense_variant 0.88
rpoC 765230 p.Ala621Thr missense_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 0.92
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416789 p.Ala187Pro missense_variant 0.96
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
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 0.94
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2222308 p.Asp286Gly missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.95
ahpC 2726051 c.-142G>A upstream_gene_variant 0.95
folC 2746515 c.1084C>T synonymous_variant 0.23
Rv2752c 3064632 c.1560C>T synonymous_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.89
fprA 3475159 p.Asn385Asp missense_variant 0.79
whiB7 3568816 c.-137C>T upstream_gene_variant 0.87
alr 3840689 c.732C>T synonymous_variant 0.18
alr 3841253 c.168C>T synonymous_variant 0.99
alr 3841277 c.144C>T synonymous_variant 0.99
clpC1 4040517 p.Val63Ala missense_variant 0.97
embC 4240671 p.Thr270Ile missense_variant 0.98
embC 4241042 p.Asn394Asp missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.89
embB 4246548 p.Pro12Gln missense_variant 0.24
embB 4246555 c.42G>C synonymous_variant 0.23
embB 4246556 p.Ala15Pro missense_variant 0.23
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 0.92
aftB 4269606 c.-770T>C upstream_gene_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.81
gid 4407873 c.330G>T synonymous_variant 0.9
gid 4407927 p.Glu92Asp missense_variant 0.1
eis 2624690 c.-8888_*89433del transcript_ablation 1.0
eis 2635577 c.-8869_*78546del transcript_ablation 1.0
eis 2638562 c.-8888_*75561del transcript_ablation 1.0
eis 2641332 c.-8879_*72791del transcript_ablation 1.0
clpC1 3992798 c.-39483_*45359del transcript_ablation 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0