TB-Profiler result

Run: SRR6650345
Summary

Run ID: SRR6650345

Sample name:

Date: 15-08-2023 08:00:10

Number of reads: 1158718

Percentage reads mapped: 99.31

Strain: lineage1.1.3.1

Drug-resistance: Other

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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 R pncA p.Thr168Pro (0.16)
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
pncA 2288740 p.Thr168Pro missense_variant 0.16 pyrazinamide
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 6907 p.Ile556Met missense_variant 0.12
gyrB 6913 p.Asn558Lys missense_variant 0.13
gyrB 6918 p.His560Leu missense_variant 0.21
gyrA 6922 c.-380G>T upstream_gene_variant 0.27
gyrB 6927 p.Leu563Trp missense_variant 0.21
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 0.24
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575920 c.573C>T synonymous_variant 1.0
mshA 576744 p.Val466Gly missense_variant 0.17
ccsA 619831 c.-60T>G upstream_gene_variant 0.21
ccsA 620545 p.Leu219Val missense_variant 0.17
ccsA 620551 p.Asp221His missense_variant 0.25
ccsA 620564 p.Leu225Pro missense_variant 0.13
ccsA 620748 c.858T>G synonymous_variant 0.41
ccsA 620756 p.Asp289Gly missense_variant 0.33
ccsA 620773 p.Ile295Val missense_variant 0.31
rpoB 759611 c.-196G>C upstream_gene_variant 0.35
rpoB 759615 c.-192A>C upstream_gene_variant 0.24
rpoB 759620 c.-187A>C upstream_gene_variant 0.24
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
mmpR5 779336 p.Asp116Ala missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781679 c.120C>T synonymous_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.28
fbiC 1304146 p.Ile406Val missense_variant 0.16
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471658 n.-188T>C upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473932 n.275C>A non_coding_transcript_exon_variant 0.2
rrl 1473948 n.291C>A non_coding_transcript_exon_variant 0.14
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.23
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.16
ndh 2103225 c.-183A>C upstream_gene_variant 0.23
ndh 2103235 c.-193C>G upstream_gene_variant 0.23
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167660 p.Thr985Pro missense_variant 0.18
PPE35 2167686 p.Asn976Thr missense_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170082 c.531T>G synonymous_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289511 c.-270T>G upstream_gene_variant 0.19
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.31
kasA 2518151 p.Ser13Arg missense_variant 0.28
kasA 2518605 p.Val164Gly missense_variant 0.16
eis 2714559 c.774C>G synonymous_variant 0.18
eis 2714566 p.Leu256Pro missense_variant 0.18
eis 2715103 p.Leu77Pro missense_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.19
ahpC 2726269 p.Val26Gly missense_variant 0.24
ahpC 2726286 p.Gly32Arg missense_variant 0.29
ahpC 2726338 p.Val49Gly missense_variant 0.27
ahpC 2726341 p.Val50Gly missense_variant 0.29
ahpC 2726345 c.153C>T synonymous_variant 0.17
ahpC 2726350 p.Trp53Leu missense_variant 0.26
ahpC 2726355 p.Lys55Glu missense_variant 0.17
ahpC 2726360 p.Asp56Glu missense_variant 0.2
folC 2746745 p.Val285Gly missense_variant 0.18
ribD 2987316 p.Ala160Pro missense_variant 0.27
ribD 2987323 p.Val162Gly missense_variant 0.29
ribD 2987325 p.Ile163Val missense_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074645 c.-174T>G upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339279 c.162T>G synonymous_variant 0.2
fbiD 3339437 p.Ala107Val missense_variant 1.0
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 0.92
whiB7 3568417 p.Lys88Arg missense_variant 0.14
Rv3236c 3611964 p.Asn385His missense_variant 0.2
Rv3236c 3612975 p.Ile48Val missense_variant 0.12
fbiB 3642223 p.Arg230Gln missense_variant 1.0
alr 3841253 c.168C>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240655 p.Ala265Pro missense_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 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.19
embA 4243365 p.Trp45Gly missense_variant 0.15
embA 4243372 p.Gln47Arg missense_variant 0.17
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 0.2
embB 4249329 p.Met939Thr missense_variant 0.13
aftB 4268744 c.93A>G synonymous_variant 0.18
aftB 4268776 p.Ser21Gly missense_variant 0.41
aftB 4268786 c.51C>T synonymous_variant 0.16
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269479 p.Met119Val missense_variant 0.2
ubiA 4269484 p.Ala117Gly missense_variant 0.2
aftB 4269486 c.-650T>G upstream_gene_variant 0.2
ubiA 4269502 p.Val111Gly missense_variant 0.2
aftB 4269504 c.-668A>G upstream_gene_variant 0.2
ubiA 4269511 p.Val108Gly missense_variant 0.18
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
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0