TB-Profiler result

Run: SRR6650391
Summary

Run ID: SRR6650391

Sample name:

Date: 15-08-2023 08:01:50

Number of reads: 1296455

Percentage reads mapped: 99.3

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 0.99
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 6913 p.Asn558Lys missense_variant 0.15
gyrA 6922 c.-380G>T upstream_gene_variant 0.17
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 490751 c.-32T>G upstream_gene_variant 0.18
fgd1 490759 c.-24A>T upstream_gene_variant 0.27
fgd1 490771 c.-12T>G upstream_gene_variant 0.23
fgd1 490784 p.Val1Gly missense_variant 0.18
fgd1 490787 p.Ala2Gly missense_variant 0.18
fgd1 491027 p.Asn82Thr missense_variant 0.19
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576720 p.Glu458Gly missense_variant 0.15
mshA 576723 p.Val459Gly missense_variant 0.17
ccsA 620537 p.Val216Gly missense_variant 0.16
ccsA 620551 p.Asp221His missense_variant 0.27
ccsA 620748 c.858T>G synonymous_variant 0.21
ccsA 620756 p.Asp289Gly missense_variant 0.17
ccsA 620761 p.Lys291Gln missense_variant 0.13
rpoB 759611 c.-196G>C upstream_gene_variant 0.22
rpoB 759615 c.-192A>C upstream_gene_variant 0.33
rpoB 759618 c.-189T>C upstream_gene_variant 0.17
rpoB 759620 c.-187A>C upstream_gene_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 777572 c.909C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.21
fbiC 1303016 p.Val29Gly missense_variant 0.2
fbiC 1304159 p.Val410Gly missense_variant 0.21
fbiC 1304166 c.1236A>G synonymous_variant 0.19
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461101 c.57T>G synonymous_variant 0.22
atpE 1461119 c.75T>G synonymous_variant 0.24
atpE 1461125 c.81T>G synonymous_variant 0.18
atpE 1461131 c.87T>G synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918066 p.Ala43Pro missense_variant 0.17
ndh 2103225 c.-183A>C upstream_gene_variant 0.24
ndh 2103235 c.-193C>G upstream_gene_variant 0.16
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 2169314 p.Asn433Lys missense_variant 0.16
PPE35 2169317 c.1296C>T synonymous_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289380 c.-139G>T upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.25
kasA 2518151 p.Ser13Arg missense_variant 0.27
eis 2714549 p.Met262Leu missense_variant 0.16
eis 2714566 p.Leu256Pro missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.15
ahpC 2726269 p.Val26Gly missense_variant 0.19
ahpC 2726279 c.87G>A synonymous_variant 0.15
ahpC 2726338 p.Val49Gly missense_variant 0.35
ahpC 2726341 p.Val50Gly missense_variant 0.4
ahpC 2726343 p.Phe51Val missense_variant 0.15
ahpC 2726350 p.Trp53Leu missense_variant 0.42
ahpC 2726360 p.Asp56Glu missense_variant 0.15
ahpC 2726366 c.174G>C synonymous_variant 0.15
ribD 2987316 p.Ala160Pro missense_variant 0.14
ribD 2987323 p.Val162Gly missense_variant 0.23
ribD 2987325 p.Ile163Val missense_variant 0.19
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074641 c.-170C>T upstream_gene_variant 0.27
thyA 3074645 c.-174T>G upstream_gene_variant 0.27
thyA 3074648 c.-177T>G upstream_gene_variant 0.29
thyA 3074652 c.-181T>G upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449093 p.Ala197Gly missense_variant 0.18
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 3612835 c.282T>G synonymous_variant 0.22
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
clpC1 4039435 p.Phe424Val missense_variant 0.16
clpC1 4039471 p.Ile412Val missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.18
embA 4243372 p.Gln47Arg missense_variant 0.18
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244641 p.Val470Gly missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249314 p.Phe934Ser missense_variant 0.18
embB 4249323 p.Ala937Glu missense_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269502 p.Val111Gly missense_variant 0.19
aftB 4269504 c.-668A>G upstream_gene_variant 0.24
ubiA 4269511 p.Val108Gly missense_variant 0.33
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326887 p.Asp196Gly missense_variant 0.16
ethR 4326898 c.-651C>G upstream_gene_variant 0.15
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