TB-Profiler result

Run: SRR6650235
Summary

Run ID: SRR6650235

Sample name:

Date: 15-08-2023 07:58:17

Number of reads: 492014

Percentage reads mapped: 99.45

Strain: lineage3

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
Streptomycin
Fluoroquinolones R gyrA p.Asp94Tyr (0.42)
Moxifloxacin R gyrA p.Asp94Tyr (0.42)
Ofloxacin R gyrA p.Asp94Tyr (0.42)
Levofloxacin R gyrA p.Asp94Tyr (0.42)
Ciprofloxacin R gyrA p.Asp94Tyr (0.42)
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
lineage3 East-African-Indian CAS RD750 0.77
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
gyrA 7581 p.Asp94Tyr missense_variant 0.42 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 0.15
gyrB 6912 p.Asn558Arg missense_variant 0.29
gyrB 6918 p.His560Leu missense_variant 0.29
gyrA 6922 c.-380G>T upstream_gene_variant 0.33
gyrB 6929 p.Ala564Pro missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.17
gyrA 9143 c.1842T>C synonymous_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490979 p.Asn66Thr missense_variant 0.29
fgd1 491008 p.Thr76Pro missense_variant 0.29
fgd1 491014 p.Thr78Pro missense_variant 0.36
fgd1 491027 p.Asn82Thr missense_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576689 p.Tyr448Asp missense_variant 0.29
mshA 576723 p.Val459Gly missense_variant 0.33
ccsA 619713 c.-178C>G upstream_gene_variant 0.2
ccsA 619835 c.-56G>T upstream_gene_variant 0.2
ccsA 619839 c.-52C>G upstream_gene_variant 0.22
ccsA 619844 c.-47T>G upstream_gene_variant 0.2
ccsA 619851 c.-40A>G upstream_gene_variant 0.18
ccsA 619870 c.-21A>C upstream_gene_variant 0.17
ccsA 619884 c.-7A>G upstream_gene_variant 0.18
ccsA 620748 c.858T>G synonymous_variant 0.38
ccsA 620752 p.Arg288Gly missense_variant 0.25
ccsA 620756 p.Asp289Gly missense_variant 0.3
ccsA 620761 p.Lys291Gln missense_variant 0.22
ccsA 620770 p.Trp294Arg missense_variant 0.22
ccsA 620779 p.Val297Ile missense_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 0.57
rpoB 759754 c.-53A>C upstream_gene_variant 0.22
rpoB 759808 c.2T>G start_lost 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763849 c.480G>A synonymous_variant 0.25
rpoC 765171 p.Pro601Leu missense_variant 0.43
rpoC 765230 p.Ala621Thr missense_variant 0.43
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775643 c.2838A>C synonymous_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777431 c.1050A>C synonymous_variant 0.22
mmpR5 779336 p.Asp116Ala missense_variant 0.5
mmpR5 779348 p.Val120Gly missense_variant 0.43
mmpR5 779356 p.Arg123Gly missense_variant 0.5
mmpR5 779363 p.Leu125Arg missense_variant 0.45
mmpR5 779371 p.Ala128Pro missense_variant 0.45
rpsL 781363 c.-197T>G upstream_gene_variant 0.43
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800988 c.180C>A synonymous_variant 0.27
rplC 800997 p.Asn63Lys missense_variant 0.27
embR 1416816 p.Ala178Thr missense_variant 0.73
embR 1417019 p.Cys110Tyr missense_variant 0.57
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.4
rrl 1475029 n.1372T>G non_coding_transcript_exon_variant 0.29
fabG1 1673668 p.Glu77Lys missense_variant 0.33
fabG1 1673690 p.Val84Gly missense_variant 0.29
fabG1 1674049 p.Gln204Lys missense_variant 0.15
fabG1 1674076 p.Thr213Pro missense_variant 0.36
inhA 1674892 p.Asn231Asp missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918391 p.Val151Gly missense_variant 0.33
tlyA 1918403 p.Leu155Pro missense_variant 0.27
tlyA 1918419 p.Leu160Phe missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154726 c.1386C>A synonymous_variant 0.29
katG 2155856 p.Thr86Pro missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.38
PPE35 2169266 c.1347C>G synonymous_variant 0.22
PPE35 2169278 c.1335T>G synonymous_variant 0.25
PPE35 2169285 p.Tyr443Phe missense_variant 0.29
PPE35 2169293 c.1320T>G synonymous_variant 0.67
PPE35 2169296 p.Asn439Lys missense_variant 0.25
PPE35 2169299 p.Asn438Lys missense_variant 0.38
PPE35 2169303 p.Met437Lys missense_variant 0.25
PPE35 2169306 p.Asp436Gly missense_variant 0.25
PPE35 2169314 p.Asn433Lys missense_variant 0.25
PPE35 2169317 c.1296C>T synonymous_variant 0.5
PPE35 2169320 p.Leu431Phe missense_variant 0.22
PPE35 2169854 c.759T>G synonymous_variant 0.2
PPE35 2170390 p.Trp75Gly missense_variant 0.25
PPE35 2170407 p.Ala69Gly missense_variant 0.22
PPE35 2170422 p.Ala64Gly missense_variant 0.22
PPE35 2170425 p.Val63Gly missense_variant 0.2
PPE35 2170436 c.177T>G synonymous_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223361 c.-197C>T upstream_gene_variant 0.83
pncA 2289047 c.195C>T synonymous_variant 0.83
pncA 2289365 c.-125delC upstream_gene_variant 0.77
kasA 2518147 c.33C>T synonymous_variant 0.33
kasA 2518151 p.Ser13Arg missense_variant 0.25
eis 2715103 p.Leu77Pro missense_variant 0.6
eis 2715117 c.216T>G synonymous_variant 0.29
ahpC 2726105 c.-88G>A upstream_gene_variant 0.83
ahpC 2726640 p.Thr150Pro missense_variant 0.2
folC 2746655 p.Ala315Gly missense_variant 0.9
folC 2746714 c.885T>G synonymous_variant 0.22
folC 2746745 p.Val285Gly missense_variant 0.25
pepQ 2859438 c.981T>G synonymous_variant 0.25
pepQ 2859502 p.Pro306Arg missense_variant 0.18
pepQ 2859904 p.Val172Gly missense_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 0.45
Rv2752c 3064677 p.Glu505Asp missense_variant 0.44
thyX 3068024 c.-79A>C upstream_gene_variant 0.25
thyX 3068031 c.-86A>C upstream_gene_variant 0.27
thyX 3068042 c.-97T>C upstream_gene_variant 0.22
thyX 3068051 c.-106A>C upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339188 p.Thr24Asn missense_variant 0.15
fbiD 3339273 c.156T>G synonymous_variant 0.38
fbiD 3339279 c.162T>G synonymous_variant 0.25
fbiD 3339281 p.Ser55Leu missense_variant 0.38
Rv3083 3449079 p.Leu192Phe missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.5
Rv3236c 3612113 p.Glu335Gly missense_variant 0.29
Rv3236c 3612752 p.Ala122Gly missense_variant 0.25
Rv3236c 3612772 c.345T>G synonymous_variant 0.33
Rv3236c 3612776 p.Asp114Gly missense_variant 0.38
Rv3236c 3612780 p.Leu113Val missense_variant 0.25
Rv3236c 3612784 p.Leu111Phe missense_variant 0.25
Rv3236c 3612789 p.Leu110Val missense_variant 0.25
Rv3236c 3612793 c.324C>G synonymous_variant 0.57
Rv3236c 3612800 p.Val106Gly missense_variant 0.29
Rv3236c 3612805 c.312T>G synonymous_variant 0.38
fbiB 3641817 p.Thr95Pro missense_variant 0.17
fbiB 3642738 p.Ile402Phe missense_variant 0.17
fbiB 3642744 p.Ala404Ser missense_variant 0.27
fbiB 3642751 p.Asp406Ala missense_variant 0.36
fbiB 3642753 c.1219C>T synonymous_variant 0.25
fbiB 3642764 p.Asp410Glu missense_variant 0.14
alr 3841253 c.168C>T synonymous_variant 0.47
alr 3841473 c.-53G>A upstream_gene_variant 0.71
alr 3841506 c.-86A>C upstream_gene_variant 0.29
alr 3841528 c.-108A>C upstream_gene_variant 0.19
clpC1 4039916 c.789T>G synonymous_variant 0.25
embC 4239973 c.111T>G synonymous_variant 0.27
embC 4239995 p.Ile45Leu missense_variant 0.2
embC 4240001 p.Thr47Pro missense_variant 0.22
embC 4240006 c.144A>C synonymous_variant 0.38
embC 4241042 p.Asn394Asp missense_variant 0.43
embC 4242075 p.Arg738Gln missense_variant 0.7
embC 4242212 p.Ala784Pro missense_variant 0.29
embC 4242220 c.2358A>C synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.27
embC 4242893 p.Ile1011Val missense_variant 0.33
embC 4242903 p.Asp1014Gly missense_variant 0.29
embA 4243361 c.129C>T synonymous_variant 0.2
embA 4243365 p.Trp45Gly missense_variant 0.2
embA 4243699 p.Pro156Leu missense_variant 0.7
embA 4243848 p.Val206Met missense_variant 0.33
embA 4243971 p.Gly247* stop_gained 0.14
embA 4245969 p.Pro913Ser missense_variant 0.5
embB 4247623 c.1110G>C synonymous_variant 0.3
embB 4247646 p.Glu378Ala missense_variant 0.3
embB 4248663 p.Val717Gly missense_variant 0.27
embB 4248677 p.Met722Leu missense_variant 0.17
embB 4248689 p.Ile726Val missense_variant 0.18
embB 4248725 p.Ser738Ala missense_variant 0.23
embB 4248728 p.Asn739His missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 0.2
ubiA 4269848 c.-15A>G upstream_gene_variant 0.21
ubiA 4269856 c.-23G>A upstream_gene_variant 0.2
ubiA 4269864 c.-31C>G upstream_gene_variant 0.4
ethR 4326874 c.-675C>T upstream_gene_variant 0.33
ethA 4326887 p.Asp196Gly missense_variant 0.25
ethR 4326898 c.-651C>G upstream_gene_variant 0.22
ethR 4327628 p.Leu27Arg missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.4
gid 4407873 c.330G>T synonymous_variant 0.22
gid 4407955 p.Arg83Leu missense_variant 0.14