TB-Profiler result

Run: SRR5341295
Summary

Run ID: SRR5341295

Sample name:

Date: 20-10-2023 18:51:39

Number of reads: 2281347

Percentage reads mapped: 91.63

Strain: lineage1.2.2.2

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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.96
lineage1.2.2.2 Indo-Oceanic NA RD239 0.97
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 5075 c.-165C>T upstream_gene_variant 0.93
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.98
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490666 c.-117G>T upstream_gene_variant 0.91
fgd1 490678 c.-105_-104insG upstream_gene_variant 0.85
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 0.97
rpoC 763886 c.517C>A synonymous_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.16
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.15
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.17
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.21
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.29
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.3
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.35
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.36
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.36
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.31
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.3
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.22
rrs 1472253 n.408G>C non_coding_transcript_exon_variant 0.22
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.25
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.29
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.34
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.41
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.39
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.38
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.41
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.39
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.42
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.42
rrs 1472606 n.761C>T non_coding_transcript_exon_variant 0.42
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.3
rrs 1472645 n.800G>A non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.23
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.18
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.21
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.28
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.28
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.27
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.27
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.28
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.27
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.25
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.24
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.22
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.27
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.26
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.26
rrs 1472969 n.1125delC non_coding_transcript_exon_variant 0.19
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.17
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.22
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.22
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.23
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.25
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.26
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.24
rrs 1473054 n.1209C>T non_coding_transcript_exon_variant 0.12
rrl 1475687 n.2030C>A non_coding_transcript_exon_variant 1.0
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.17
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.17
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.16
rrl 1475880 n.2223C>G non_coding_transcript_exon_variant 0.15
rrl 1475881 n.2224T>G non_coding_transcript_exon_variant 0.14
rrl 1475882 n.2225C>G non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.15
rrl 1475895 n.2238C>A non_coding_transcript_exon_variant 0.17
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.17
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.16
rrl 1475920 n.2263G>C non_coding_transcript_exon_variant 0.13
rrl 1475924 n.2267A>G non_coding_transcript_exon_variant 0.14
rrl 1475933 n.2276C>G non_coding_transcript_exon_variant 0.14
rrl 1475939 n.2282G>C non_coding_transcript_exon_variant 0.13
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.22
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.26
rrl 1476265 n.2608G>A non_coding_transcript_exon_variant 0.3
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.34
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.31
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.32
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.32
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.32
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.32
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.39
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.39
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.39
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.51
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.55
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.54
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.55
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.48
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.51
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.52
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.5
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.46
rrl 1476427 n.2770G>T non_coding_transcript_exon_variant 0.44
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.46
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.42
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.39
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.26
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.96
Rv1979c 2222308 p.Asp286Gly missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.98
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.92
Rv3083 3448714 p.Asp71His missense_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.96
clpC1 4040517 p.Val63Ala missense_variant 0.96
embC 4240671 p.Thr270Ile missense_variant 0.95
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.99
embA 4246345 p.Arg1038His missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.93
ubiA 4269387 p.Glu149Asp missense_variant 0.98
aftB 4269606 c.-770T>C upstream_gene_variant 0.96
ethA 4326148 c.1326G>T synonymous_variant 0.97
ethA 4326330 p.Tyr382Asn missense_variant 0.99
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 0.91
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.93
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407715 p.Lys163Thr missense_variant 0.98
gid 4407848 p.Ala119Thr missense_variant 0.95
gid 4407873 c.330G>T synonymous_variant 0.96
gid 4408443 c.-241C>A upstream_gene_variant 0.99