TB-Profiler result

Run: SRR6650127
Summary

Run ID: SRR6650127

Sample name:

Date: 15-08-2023 07:56:13

Number of reads: 646521

Percentage reads mapped: 99.27

Strain:

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
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.98
lineage1.2.2.2 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 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 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9585 p.Leu762Val missense_variant 0.25
fgd1 491008 p.Thr76Pro missense_variant 0.2
fgd1 491014 p.Thr78Pro missense_variant 0.29
fgd1 491027 p.Asn82Thr missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575886 p.Leu180Arg missense_variant 0.2
mshA 576489 p.Val381Gly missense_variant 0.25
mshA 576723 p.Val459Gly missense_variant 0.33
ccsA 619707 c.-184T>G upstream_gene_variant 0.3
ccsA 619738 c.-153T>G upstream_gene_variant 0.25
ccsA 619831 c.-60T>G upstream_gene_variant 0.29
ccsA 619844 c.-47T>G upstream_gene_variant 0.33
ccsA 620135 p.Ala82Gly missense_variant 0.22
ccsA 620545 p.Leu219Val missense_variant 0.33
ccsA 620586 c.696C>T synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.38
ccsA 620752 p.Arg288Gly missense_variant 0.29
ccsA 620756 p.Asp289Gly missense_variant 0.22
rpoB 759792 c.-15C>T upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763849 c.480G>A synonymous_variant 0.17
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764147 p.Ser260Ala missense_variant 0.17
rpoC 765889 c.2520C>T 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 778239 p.Val81Gly missense_variant 0.2
mmpL5 778252 p.His77Asn missense_variant 0.15
mmpS5 778899 p.Gly3* stop_gained 0.15
mmpR5 779346 p.Asp119Glu missense_variant 0.15
mmpR5 779348 p.Val120Gly missense_variant 0.25
mmpR5 779356 p.Arg123Gly missense_variant 0.27
mmpR5 779363 p.Leu125Arg missense_variant 0.33
mmpR5 779369 p.Asp127Ala missense_variant 0.2
mmpR5 779371 p.Ala128Pro missense_variant 0.4
rpsL 781363 c.-197T>G upstream_gene_variant 0.57
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801276 c.468G>C synonymous_variant 0.2
rplC 801287 p.Val160Gly missense_variant 0.25
fbiC 1302948 c.18T>G synonymous_variant 1.0
Rv1258c 1406452 p.Thr297Pro missense_variant 0.43
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417480 c.-133G>T upstream_gene_variant 0.67
atpE 1461083 c.39T>G synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673668 p.Glu77Lys missense_variant 0.29
inhA 1673679 c.-523T>G upstream_gene_variant 0.29
fabG1 1674076 p.Thr213Pro missense_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918403 p.Leu155Pro missense_variant 0.17
tlyA 1918410 c.471C>T synonymous_variant 0.27
tlyA 1918431 p.Leu164Phe missense_variant 0.25
tlyA 1918435 p.Ala166Pro missense_variant 0.15
ndh 2103225 c.-183A>C upstream_gene_variant 0.18
ndh 2103235 c.-193C>G upstream_gene_variant 0.18
katG 2153914 p.Asn733Thr missense_variant 0.2
katG 2153925 p.Asp729Glu missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155856 p.Thr86Pro missense_variant 0.19
PPE35 2167828 p.Ala929Pro 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 2169285 p.Tyr443Phe missense_variant 0.17
PPE35 2169317 c.1296C>T synonymous_variant 0.25
PPE35 2169854 c.759T>G synonymous_variant 0.3
PPE35 2169934 p.Ile227Val missense_variant 1.0
PPE35 2170082 c.531T>G synonymous_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289386 c.-145A>C upstream_gene_variant 0.23
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518138 p.Asn8Lys missense_variant 0.17
eis 2715103 p.Leu77Pro missense_variant 0.21
eis 2715396 c.-64G>T upstream_gene_variant 0.25
eis 2715411 c.-79A>C upstream_gene_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726269 p.Val26Gly missense_variant 0.67
ahpC 2726277 p.Lys29Gln missense_variant 0.6
ahpC 2726286 p.Gly32Arg missense_variant 0.29
ahpC 2726502 p.Lys104Gln missense_variant 0.22
ahpC 2726506 p.Thr105Lys missense_variant 0.17
ahpC 2726519 c.327G>C synonymous_variant 0.17
folC 2747753 c.-155G>A upstream_gene_variant 1.0
pepQ 2859377 p.Thr348Ala missense_variant 0.27
pepQ 2859414 c.1005T>G synonymous_variant 0.18
pepQ 2859425 p.Gly332Arg missense_variant 0.18
pepQ 2859454 p.Val322Gly missense_variant 0.23
pepQ 2859495 p.Ile308Met missense_variant 0.15
pepQ 2860068 c.351G>A synonymous_variant 0.15
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
Rv2752c 3066103 p.Asn30Ser missense_variant 1.0
thyA 3073829 p.Gln215Lys missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.42
fbiD 3339279 c.162T>G synonymous_variant 0.31
fbiD 3339281 p.Ser55Leu missense_variant 0.23
fbiD 3339291 c.174G>C synonymous_variant 0.17
fbiD 3339310 p.Asp65His missense_variant 0.18
fbiD 3339328 p.Ala71Thr missense_variant 1.0
fbiD 3339583 p.Thr156Pro missense_variant 0.25
fbiD 3339593 p.His159Pro missense_variant 0.38
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449079 p.Leu192Phe missense_variant 0.29
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 3475280 p.Val425Gly missense_variant 0.25
Rv3236c 3611974 p.Ala381Pro missense_variant 0.21
Rv3236c 3611988 p.Leu377Val missense_variant 0.25
Rv3236c 3612384 p.Phe245Val missense_variant 0.22
Rv3236c 3612388 c.729T>G synonymous_variant 0.22
Rv3236c 3612422 p.Val232Gly missense_variant 0.2
Rv3236c 3612541 p.Leu192Phe missense_variant 0.18
fbiA 3641336 p.Val265Ala missense_variant 0.14
fbiB 3642751 p.Asp406Ala missense_variant 1.0
fbiB 3642769 p.Leu412Arg missense_variant 1.0
fbiB 3642772 p.Asp413Ala missense_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.23
alr 3841509 c.-89A>C upstream_gene_variant 0.38
alr 3841546 c.-126C>A upstream_gene_variant 1.0
ddn 3986919 p.Thr26Pro missense_variant 0.23
clpC1 4038857 c.1848C>A synonymous_variant 0.5
clpC1 4038880 p.Gln609Lys missense_variant 0.29
clpC1 4039916 c.789T>G synonymous_variant 0.23
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.36
embC 4240001 p.Thr47Pro missense_variant 0.3
embC 4240006 c.144A>C synonymous_variant 0.36
embC 4240008 p.Leu49Pro missense_variant 0.22
embC 4240017 p.Val52Gly missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242170 p.Thr770Pro missense_variant 0.25
embC 4242180 p.Leu773Trp missense_variant 0.29
embC 4242186 p.Asp775Ala missense_variant 0.29
embC 4242220 c.2358A>C synonymous_variant 0.4
embC 4242223 c.2361C>A synonymous_variant 0.33
embC 4242390 p.Leu843Arg missense_variant 0.15
embC 4242393 p.Asp844Ala missense_variant 0.18
embA 4242406 c.-827A>C upstream_gene_variant 0.2
embC 4242414 p.Leu851Arg missense_variant 0.3
embC 4242422 p.Trp854Gly missense_variant 0.2
embC 4242425 p.Arg855Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.25
embA 4242901 c.-332G>C upstream_gene_variant 0.18
embC 4242908 p.Phe1016Val missense_variant 0.18
embA 4242931 c.-302G>C upstream_gene_variant 0.15
embA 4244653 p.Gln474Pro missense_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247616 p.Glu368Gly missense_variant 0.21
embB 4247623 c.1110G>C synonymous_variant 0.27
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248799 c.2286T>G synonymous_variant 0.27
embB 4249305 p.Asn931Thr missense_variant 0.22
embB 4249314 p.Phe934Ser missense_variant 0.22
embB 4249322 p.Ala937Lys missense_variant 0.38
embB 4249330 p.Met939Ile missense_variant 0.25
aftB 4267637 c.1200C>T synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269828 p.Ser2Arg missense_variant 0.33
ubiA 4269833 c.1A>G start_lost 0.2
ubiA 4269848 c.-15A>G upstream_gene_variant 0.31
ubiA 4269856 c.-23G>A upstream_gene_variant 0.17
ubiA 4269864 c.-31C>G upstream_gene_variant 0.55
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4326876 p.Lys200Gln missense_variant 0.17
ethA 4326887 p.Asp196Gly missense_variant 0.42
ethA 4326903 p.Val191Leu missense_variant 0.21
ethA 4326905 p.Leu190Pro missense_variant 0.29
ethR 4327624 p.Glu26Lys missense_variant 0.15
ethR 4327634 p.Ile29Thr missense_variant 0.2
ethR 4327637 p.Leu30Pro missense_variant 0.33
ethR 4327642 p.Thr32Pro missense_variant 0.33
ethR 4327813 p.Thr89Pro missense_variant 0.36
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