TB-Profiler result

Run: SRR6650319
Summary

Run ID: SRR6650319

Sample name:

Date: 15-08-2023 08:00:20

Number of reads: 1552340

Percentage reads mapped: 99.52

Strain: lineage1.1.3.1

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 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
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 1.0
gyrB 6929 p.Ala564Pro missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7555 p.His85Arg missense_variant 0.12
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
gyrA 9795 p.Gly832Arg missense_variant 1.0
fgd1 491014 p.Thr78Pro missense_variant 0.28
fgd1 491027 p.Asn82Thr missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.21
ccsA 620756 p.Asp289Gly missense_variant 0.35
ccsA 620770 p.Trp294Arg missense_variant 0.19
ccsA 620773 p.Ile295Val missense_variant 0.17
ccsA 620778 p.Asn296Lys missense_variant 0.24
ccsA 620801 p.Val304Gly missense_variant 0.2
rpoB 759611 c.-196G>C upstream_gene_variant 0.25
rpoB 759615 c.-192A>C upstream_gene_variant 0.19
rpoB 759620 c.-187A>C upstream_gene_variant 0.25
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776974 p.Met503Val missense_variant 1.0
mmpR5 779336 p.Asp116Ala missense_variant 0.23
mmpR5 779348 p.Val120Gly missense_variant 0.15
mmpR5 779369 p.Asp127Ala missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.21
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461083 c.39T>G synonymous_variant 0.31
atpE 1461101 c.57T>G synonymous_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474023 n.366T>G non_coding_transcript_exon_variant 0.2
rrl 1474452 n.795C>T non_coding_transcript_exon_variant 0.18
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.4
rrl 1476155 n.2498C>T non_coding_transcript_exon_variant 0.13
fabG1 1674076 p.Thr213Pro missense_variant 0.26
rpsA 1833978 p.Gly146Val missense_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918010 p.Ala24Gly missense_variant 0.17
tlyA 1918044 p.Asp35Glu missense_variant 0.17
tlyA 1918052 p.Pro38Arg missense_variant 0.25
tlyA 1918061 p.Lys41Thr missense_variant 0.14
ndh 2103225 c.-183A>C upstream_gene_variant 0.17
ndh 2103235 c.-193C>G upstream_gene_variant 0.25
katG 2153923 p.Lys730Arg missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169848 p.Asn255Lys missense_variant 0.19
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 2518147 c.33C>T synonymous_variant 0.25
kasA 2518192 c.78G>C synonymous_variant 0.18
kasA 2518323 p.Ser70Asn missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.19
ahpC 2726338 p.Val49Gly missense_variant 0.24
ahpC 2726341 p.Val50Gly missense_variant 0.29
ahpC 2726343 p.Phe51Val missense_variant 0.17
ahpC 2726350 p.Trp53Leu missense_variant 0.2
ahpC 2726358 p.Asp56Lys missense_variant 0.15
ahpC 2726617 p.Asn142Thr missense_variant 0.21
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065575 p.Ala206Val missense_variant 1.0
thyA 3074641 c.-170C>T upstream_gene_variant 0.21
thyA 3074645 c.-174T>G upstream_gene_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.21
fbiD 3339593 p.His159Pro missense_variant 0.18
fbiD 3339626 p.His170Pro missense_variant 0.17
fbiD 3339688 p.Thr191Pro missense_variant 0.39
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
Rv3236c 3612805 c.312T>G synonymous_variant 0.19
alr 3841253 c.168C>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 0.97
embC 4240006 c.144A>C synonymous_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.19
embA 4243398 p.Thr56Pro missense_variant 0.21
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.19
aftB 4268776 p.Ser21Gly missense_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 0.94
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327642 p.Thr32Pro missense_variant 0.19
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0