TB-Profiler result

Run: SRR6650175
Summary

Run ID: SRR6650175

Sample name:

Date: 15-08-2023 07:56:38

Number of reads: 677787

Percentage reads mapped: 99.34

Strain: lineage1.2.2.2

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
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.99
lineage1.2.2.2 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 5530 c.291C>T synonymous_variant 1.0
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 7994 c.693C>T synonymous_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 490759 c.-24A>T upstream_gene_variant 0.17
fgd1 491014 p.Thr78Pro missense_variant 0.36
fgd1 491027 p.Asn82Thr missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575704 c.357T>G synonymous_variant 0.15
mshA 576705 p.Gln453Pro missense_variant 0.18
mshA 576723 p.Val459Gly missense_variant 0.25
ccsA 619831 c.-60T>G upstream_gene_variant 0.18
ccsA 620586 c.696C>T synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.33
ccsA 620752 p.Arg288Gly missense_variant 0.31
ccsA 620756 p.Asp289Gly missense_variant 0.38
ccsA 620759 p.Arg290Pro missense_variant 0.14
ccsA 620763 c.873G>A synonymous_variant 0.15
ccsA 620773 p.Ile295Val missense_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763849 c.480G>A synonymous_variant 0.22
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777155 c.1326G>C synonymous_variant 1.0
mmpL5 779277 c.-797C>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.15
rplC 801274 p.Thr156Pro missense_variant 0.19
fbiC 1302948 c.18T>G synonymous_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.2
fbiC 1304703 c.1773C>G synonymous_variant 0.12
Rv1258c 1406464 p.Thr293Ala missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461101 c.57T>G synonymous_variant 0.29
atpE 1461119 c.75T>G synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474452 n.795C>T non_coding_transcript_exon_variant 0.25
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 1.0
inhA 1673679 c.-523T>G upstream_gene_variant 0.3
fabG1 1673690 p.Val84Gly missense_variant 0.33
fabG1 1674076 p.Thr213Pro missense_variant 0.2
inhA 1674864 c.663C>G synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917989 p.Ala17Gly missense_variant 0.2
tlyA 1918015 p.Leu26Val missense_variant 0.22
tlyA 1918036 p.Arg33Gly missense_variant 0.29
tlyA 1918069 p.Thr44Pro missense_variant 0.29
ndh 2102536 c.507G>A synonymous_variant 0.27
ndh 2102540 p.Ala168Gly missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169854 c.759T>G synonymous_variant 0.23
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 0.22
pncA 2289753 c.-512T>G upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.3
kasA 2518151 p.Ser13Arg missense_variant 0.22
kasA 2518155 p.Val14Gly missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746136 c.1463G>T stop_lost&splice_region_variant 0.15
pepQ 2859400 p.Asp340Gly missense_variant 0.33
pepQ 2859438 c.981T>G synonymous_variant 0.25
ribD 2987316 p.Ala160Pro missense_variant 0.17
ribD 2987323 p.Val162Gly missense_variant 0.33
ribD 2987325 p.Ile163Val missense_variant 0.25
ribD 2987337 p.Gly167Arg missense_variant 0.4
ribD 2987344 p.Asp169Gly missense_variant 0.2
ribD 2987444 p.Phe202Leu missense_variant 0.13
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
Rv2752c 3065829 p.Ile121Met missense_variant 1.0
Rv2752c 3066103 p.Asn30Ser missense_variant 1.0
thyA 3074613 c.-142C>G upstream_gene_variant 0.22
thyA 3074617 c.-146G>T upstream_gene_variant 0.18
thyA 3074641 c.-170C>T upstream_gene_variant 0.36
thyA 3074645 c.-174T>G upstream_gene_variant 0.36
thyA 3074648 c.-177T>G upstream_gene_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449072 p.Val190Gly missense_variant 0.23
Rv3083 3449079 p.Leu192Phe missense_variant 0.18
Rv3083 3449098 p.Ser199Pro missense_variant 0.18
Rv3083 3449110 p.Ser203Arg missense_variant 0.2
fprA 3473903 c.-104A>G upstream_gene_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
fprA 3475270 p.His422Asp missense_variant 1.0
whiB7 3568402 c.278A>G stop_lost&splice_region_variant 0.17
whiB7 3568419 c.261C>A synonymous_variant 0.18
whiB7 3568425 c.255T>C synonymous_variant 0.25
whiB7 3568431 c.249C>G synonymous_variant 0.18
Rv3236c 3612780 p.Leu113Val missense_variant 0.36
Rv3236c 3612811 c.306G>C synonymous_variant 0.18
Rv3236c 3612835 c.282T>G synonymous_variant 0.17
alr 3841506 c.-86A>C upstream_gene_variant 0.22
alr 3841509 c.-89A>C upstream_gene_variant 0.22
alr 3841543 c.-123C>T upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 1.0
clpC1 4039471 p.Ile412Val missense_variant 0.3
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.33
embC 4240017 p.Val52Gly missense_variant 0.17
embC 4240655 p.Ala265Pro missense_variant 0.2
embC 4240661 p.Trp267Arg missense_variant 0.18
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 4243888 p.Val219Gly missense_variant 0.15
embA 4245964 p.Val911Glu missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247584 c.1071C>G synonymous_variant 0.14
embB 4247616 p.Glu368Gly missense_variant 0.33
embB 4247623 c.1110G>C synonymous_variant 0.33
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247656 p.Lys381Asn missense_variant 0.18
embB 4249323 p.Ala937Glu missense_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4326887 p.Asp196Gly missense_variant 0.27
ethA 4326905 p.Leu190Pro missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0