TB-Profiler result

Run: SRR6650366
Summary

Run ID: SRR6650366

Sample name:

Date: 15-08-2023 08:24:23

Number of reads: 1964660

Percentage reads mapped: 99.2

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.95
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491008 p.Thr76Pro missense_variant 0.23
fgd1 491014 p.Thr78Pro missense_variant 0.32
fgd1 491303 p.Ile174Thr missense_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575358 p.Val4Gly missense_variant 0.22
mshA 575926 c.579A>C synonymous_variant 0.29
mshA 576744 p.Val466Gly missense_variant 0.23
ccsA 620532 c.642T>G synonymous_variant 0.3
ccsA 620748 c.858T>G synonymous_variant 0.31
rpoB 759620 c.-187A>C upstream_gene_variant 0.25
rpoB 761890 p.Val695Gly missense_variant 0.28
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 777354 p.Val376Gly missense_variant 0.24
mmpR5 779354 p.Leu122Arg missense_variant 0.17
mmpR5 779356 p.Arg123Gly missense_variant 0.22
mmpR5 779363 p.Leu125Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.29
fbiC 1304159 p.Val410Gly missense_variant 0.21
fbiC 1304317 p.Arg463Cys missense_variant 1.0
Rv1258c 1407317 c.24G>A synonymous_variant 1.0
embR 1416375 p.Val325Ile missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473372 n.1527A>T non_coding_transcript_exon_variant 0.15
rrl 1474461 n.804A>C non_coding_transcript_exon_variant 0.17
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.29
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 1.0
PPE35 2169285 p.Tyr443Phe missense_variant 0.17
PPE35 2169320 p.Leu431Phe missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170053 p.Thr187Ser missense_variant 0.19
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288682 c.560G>A splice_region_variant&stop_retained_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714566 p.Leu256Pro missense_variant 0.14
eis 2714569 p.Ala255Gly missense_variant 0.29
eis 2714768 p.Gly189Arg missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.45
ahpC 2726341 p.Val50Gly missense_variant 0.37
ahpC 2726350 p.Trp53Leu missense_variant 0.14
Rv2752c 3064632 c.1560C>T synonymous_variant 0.94
thyX 3067497 p.Leu150Arg missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
ald 3087894 c.1075C>T synonymous_variant 1.0
fbiD 3339566 p.Val150Gly missense_variant 0.24
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
fbiB 3641955 p.Gly141Arg missense_variant 0.18
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.29
alr 3841509 c.-89A>C upstream_gene_variant 0.29
alr 3841513 c.-93A>C upstream_gene_variant 0.23
clpC1 4038864 p.Val614Gly missense_variant 0.29
clpC1 4039484 c.1221T>G synonymous_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239832 c.-31T>G upstream_gene_variant 0.27
embC 4239842 c.-21C>A upstream_gene_variant 0.13
embC 4239973 c.111T>G synonymous_variant 0.19
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242414 p.Leu851Arg missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.31
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244778 p.Ser516Pro missense_variant 0.23
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249305 p.Asn931Thr missense_variant 0.26
aftB 4267999 c.838T>C synonymous_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
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
gid 4408369 c.-167G>A upstream_gene_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0