TB-Profiler result

Run: SRR11972313
Summary

Run ID: SRR11972313

Sample name:

Date: 03-04-2023 05:36:40

Number of reads: 815699

Percentage reads mapped: 98.51

Strain: lineage3.1.2;lineage1.1.3.1

Drug-resistance: RR-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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.15
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.62
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.29
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.74
lineage1.1.3.1 Indo-Oceanic NA RD239 0.18
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
rpoB 761095 p.Leu430Pro missense_variant 0.8 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.14 streptomycin
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 0.28
gyrA 6436 c.-866C>T upstream_gene_variant 0.21
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.16
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491133 c.351A>T synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576670 p.Tyr441* stop_gained 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 0.62
rpoC 762434 c.-936T>G upstream_gene_variant 0.89
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.15
rpoC 765171 p.Pro601Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.8
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155371 c.741C>T synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.21
PPE35 2168604 p.Pro670Leu missense_variant 0.53
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.71
pncA 2289365 c.-125delC upstream_gene_variant 0.74
pncA 2290053 c.-812A>T upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 0.5
ahpC 2726105 c.-88G>A upstream_gene_variant 0.48
thyA 3073791 c.681T>C synonymous_variant 0.12
ald 3086750 c.-70A>C upstream_gene_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.31
fbiB 3642851 c.1317G>A synonymous_variant 0.29
alr 3840689 c.732C>T synonymous_variant 0.18
alr 3841253 c.168C>T synonymous_variant 0.19
alr 3841277 c.144C>T synonymous_variant 0.3
clpC1 4040517 p.Val63Ala missense_variant 0.4
embC 4241042 p.Asn394Asp missense_variant 0.44
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.19
embB 4247646 p.Glu378Ala missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 0.38
aftB 4269606 c.-770T>C upstream_gene_variant 0.33
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 0.16
gid 4407793 p.Arg137Gln missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 0.2
gid 4407927 p.Glu92Asp missense_variant 0.18