TB-Profiler result

Run: SRR6650185
Summary

Run ID: SRR6650185

Sample name:

Date: 15-08-2023 08:20:25

Number of reads: 1298276

Percentage reads mapped: 99.35

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
Rifampicin
Isoniazid R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00)
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 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA RD239 1.0
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
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 5731 c.492C>T synonymous_variant 1.0
gyrB 6112 p.Met291Ile missense_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 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491014 p.Thr78Pro missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576718 c.1371C>G synonymous_variant 0.2
ccsA 620748 c.858T>G synonymous_variant 0.31
ccsA 620756 p.Asp289Gly missense_variant 0.4
ccsA 620763 c.873G>A synonymous_variant 0.2
ccsA 620773 p.Ile295Val missense_variant 0.24
ccsA 620797 p.Met303Leu missense_variant 0.16
rpoB 759611 c.-196G>C upstream_gene_variant 0.18
rpoB 759620 c.-187A>C upstream_gene_variant 0.38
rpoB 759776 c.-31T>G upstream_gene_variant 0.19
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 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766920 p.Ala1184Gly missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779348 p.Val120Gly missense_variant 0.19
mmpR5 779356 p.Arg123Gly missense_variant 0.16
mmpR5 779371 p.Ala128Pro missense_variant 0.26
mmpS5 779526 c.-621G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.94
Rv1258c 1407084 p.Val86Gly missense_variant 0.21
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461086 c.42A>G synonymous_variant 0.33
atpE 1461108 p.Ile22Leu missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473912 n.255C>G non_coding_transcript_exon_variant 0.25
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.29
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.2
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.56
rrl 1474494 n.837C>G non_coding_transcript_exon_variant 0.22
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.57
rrl 1474510 n.853T>G non_coding_transcript_exon_variant 0.4
rrl 1475029 n.1372T>G non_coding_transcript_exon_variant 0.29
fabG1 1673690 p.Val84Gly missense_variant 0.2
fabG1 1674076 p.Thr213Pro missense_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918391 p.Val151Gly missense_variant 0.19
ndh 2103225 c.-183A>C upstream_gene_variant 0.19
ndh 2103235 c.-193C>G upstream_gene_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167660 p.Thr985Pro missense_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169314 p.Asn433Lys missense_variant 0.18
PPE35 2169317 c.1296C>T synonymous_variant 0.24
PPE35 2169854 c.759T>G synonymous_variant 0.19
PPE35 2170577 c.36G>C synonymous_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.17
kasA 2518317 p.Val68Gly missense_variant 0.18
kasA 2518605 p.Val164Gly missense_variant 0.19
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726269 p.Val26Gly missense_variant 0.21
ahpC 2726286 p.Gly32Arg missense_variant 0.14
ahpC 2726506 p.Thr105Lys missense_variant 0.18
folC 2747690 c.-92G>A upstream_gene_variant 0.18
ribD 2986659 c.-180G>A upstream_gene_variant 0.22
ribD 2987323 p.Val162Gly missense_variant 0.21
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.26
Rv3083 3448714 p.Asp71His missense_variant 1.0
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 1.0
whiB7 3568401 c.279G>C stop_lost&splice_region_variant 0.2
fbiB 3642740 c.1206C>T synonymous_variant 0.18
fbiB 3642744 p.Ala404Ser missense_variant 0.19
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841528 c.-108A>C upstream_gene_variant 0.26
clpC1 4039484 c.1221T>G synonymous_variant 0.23
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.24
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.24
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 4247616 p.Glu368Gly missense_variant 0.15
embB 4247623 c.1110G>C synonymous_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.23
aftB 4268776 p.Ser21Gly missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 0.96
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269848 c.-15A>G upstream_gene_variant 0.24
ethA 4326905 p.Leu190Pro missense_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407868 p.Val112Gly missense_variant 0.95
gid 4407873 c.330G>T synonymous_variant 0.94
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0