TB-Profiler result

Run: SRR3103071
Summary

Run ID: SRR3103071

Sample name:

Date: 04-04-2023 05:02:24

Number of reads: 8498052

Percentage reads mapped: 99.2

Strain: lineage3;lineage1.1.2

Drug-resistance: Pre-XDR-TB

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
lineage3 East-African-Indian CAS RD750 0.15
lineage1 Indo-Oceanic EAI RD239 0.87
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.86
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.85
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
gyrA 7582 p.Asp94Gly missense_variant 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 0.2 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.82 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.86 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 0.91 ethambutol
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 0.86
gyrB 6124 c.885C>T synonymous_variant 0.85
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.84
gyrA 8948 c.1647G>A synonymous_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 0.87
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575932 c.585G>A synonymous_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 0.18
rpoB 760490 c.684C>T synonymous_variant 0.86
rpoB 760718 c.913_924dupGTCGGTCGCTAT conservative_inframe_insertion 0.77
rpoC 762434 c.-936T>G upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.83
rpoC 763886 c.517C>A synonymous_variant 0.84
rpoC 765171 p.Pro601Leu missense_variant 0.85
rpoC 765844 c.2475C>T synonymous_variant 0.84
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.87
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303051 p.Val41Met missense_variant 0.83
embR 1417019 p.Cys110Tyr missense_variant 0.86
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472512 n.667A>G non_coding_transcript_exon_variant 0.21
inhA 1674952 p.Pro251Ala missense_variant 0.13
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 0.86
Rv1979c 2222308 p.Asp286Gly missense_variant 0.88
Rv1979c 2223136 p.Ala10Val missense_variant 0.88
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.12
pncA 2289365 c.-125delC upstream_gene_variant 0.16
kasA 2518132 c.18C>T synonymous_variant 0.9
ahpC 2726051 c.-142G>A upstream_gene_variant 0.89
ahpC 2726105 c.-88G>A upstream_gene_variant 0.11
Rv2752c 3064632 c.1560C>T synonymous_variant 0.85
Rv2752c 3064809 c.1383C>T synonymous_variant 0.86
Rv2752c 3066271 c.-80A>G upstream_gene_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.89
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.91
fprA 3474901 p.Ser299Arg missense_variant 0.15
fprA 3475159 p.Asn385Asp missense_variant 0.85
clpC1 4040517 p.Val63Ala missense_variant 0.86
embC 4240671 p.Thr270Ile missense_variant 0.82
embC 4241042 p.Asn394Asp missense_variant 0.89
embC 4242075 p.Arg738Gln missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.87
embA 4244167 p.Ala312Val missense_variant 0.88
embA 4245969 p.Pro913Ser missense_variant 0.8
embB 4247646 p.Glu378Ala missense_variant 0.89
embB 4249000 c.2487T>G synonymous_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 0.87
aftB 4269606 c.-770T>C upstream_gene_variant 0.88
ethA 4326432 p.Leu348Phe missense_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.87
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.85
gid 4407916 p.Arg96Leu missense_variant 0.15