TB-Profiler result

Run: SRR6650161
Summary

Run ID: SRR6650161

Sample name:

Date: 15-08-2023 08:19:28

Number of reads: 563140

Percentage reads mapped: 99.32

Strain: lineage1.1.3

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.Thr177Pro (0.27)
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 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 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 2288713 p.Thr177Pro missense_variant 0.27 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 6645 p.Ser469Asn missense_variant 0.18
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 491014 p.Thr78Pro missense_variant 0.43
fgd1 491018 p.Phe79Ser missense_variant 0.29
fgd1 491027 p.Asn82Thr missense_variant 0.43
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575873 p.Thr176Pro missense_variant 0.25
mshA 575882 p.Thr179Pro missense_variant 0.29
mshA 575886 p.Leu180Arg missense_variant 0.33
mshA 576723 p.Val459Gly missense_variant 0.25
rpoB 761382 p.Thr526Pro missense_variant 0.22
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 775603 p.Thr960Pro missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.3
mmpL5 778897 c.-417A>G upstream_gene_variant 0.18
mmpL5 778907 c.-427C>G upstream_gene_variant 0.33
mmpR5 779336 p.Asp116Ala missense_variant 0.27
mmpR5 779348 p.Val120Gly missense_variant 0.4
mmpR5 779356 p.Arg123Gly missense_variant 0.3
mmpR5 779363 p.Leu125Arg missense_variant 0.36
mmpR5 779369 p.Asp127Ala missense_variant 0.18
mmpR5 779371 p.Ala128Pro missense_variant 0.27
mmpS5 779526 c.-621G>A upstream_gene_variant 1.0
rpsL 781363 c.-197T>G upstream_gene_variant 0.5
rpsL 781367 c.-193G>T upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801274 p.Thr156Pro missense_variant 0.22
rplC 801287 p.Val160Gly missense_variant 0.33
rplC 801302 p.Arg165Pro missense_variant 0.22
rplC 801316 p.Met170Val missense_variant 0.3
fbiC 1303199 p.Val90Gly missense_variant 0.3
Rv1258c 1406452 p.Thr297Pro missense_variant 0.2
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461083 c.39T>G synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471676 n.-170A>G upstream_gene_variant 0.18
rrl 1473912 n.255C>G non_coding_transcript_exon_variant 0.25
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.29
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.4
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.5
rrl 1476186 n.2529T>G non_coding_transcript_exon_variant 0.29
fabG1 1674056 p.Ile206Thr missense_variant 0.42
fabG1 1674076 p.Thr213Pro missense_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917984 c.45C>G synonymous_variant 0.18
tlyA 1917986 p.Leu16Pro missense_variant 0.17
tlyA 1918254 c.315C>T synonymous_variant 1.0
tlyA 1918410 c.471C>T synonymous_variant 0.2
ndh 2103222 c.-180A>C upstream_gene_variant 0.25
ndh 2103225 c.-183A>C upstream_gene_variant 0.22
ndh 2103235 c.-193C>G upstream_gene_variant 0.29
ndh 2103242 c.-200A>T upstream_gene_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155856 p.Thr86Pro missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169299 p.Asn438Lys missense_variant 0.27
PPE35 2169314 p.Asn433Lys missense_variant 0.19
PPE35 2169317 c.1296C>T synonymous_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288715 p.Arg176Pro missense_variant 0.18
pncA 2289386 c.-145A>C upstream_gene_variant 0.25
pncA 2289921 c.-680A>C upstream_gene_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518317 p.Val68Gly missense_variant 0.18
kasA 2518605 p.Val164Gly missense_variant 0.67
eis 2714250 c.1083T>G synonymous_variant 0.15
eis 2715560 c.-228T>G upstream_gene_variant 0.22
ahpC 2725960 c.-233A>C upstream_gene_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726257 p.Asp22Gly missense_variant 0.22
ahpC 2726265 p.Lys25Gln missense_variant 0.43
ahpC 2726269 p.Val26Gly missense_variant 0.29
ahpC 2726277 p.Lys29Gln missense_variant 0.38
ahpC 2726286 p.Gly32Arg missense_variant 0.25
ahpC 2726290 p.Asp33Gly missense_variant 0.29
ahpC 2726529 p.Asp113His missense_variant 0.21
pepQ 2859340 p.Glu360Gly missense_variant 0.18
pepQ 2859377 p.Thr348Ala missense_variant 0.27
pepQ 2859438 c.981T>G synonymous_variant 0.25
pepQ 2859454 p.Val322Gly missense_variant 0.36
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064692 c.1500T>C synonymous_variant 0.33
thyA 3073811 p.Ser221Gly missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087909 p.Thr364Pro missense_variant 0.22
fbiD 3339188 p.Thr24Asn missense_variant 0.27
fbiD 3339203 p.Val29Gly missense_variant 0.25
fbiD 3339273 c.156T>G synonymous_variant 0.21
fbiD 3339279 c.162T>G synonymous_variant 0.19
fbiD 3339310 p.Asp65His missense_variant 0.2
fbiD 3339583 p.Thr156Pro missense_variant 0.25
fbiD 3339593 p.His159Pro missense_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448765 p.Thr88Pro missense_variant 0.25
Rv3083 3449107 p.Gly202Arg missense_variant 0.22
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 3611962 p.Asn385Lys missense_variant 0.17
Rv3236c 3611974 c.1143A>C synonymous_variant 0.17
Rv3236c 3611988 p.Leu377Val missense_variant 0.23
Rv3236c 3611992 c.1125T>G synonymous_variant 0.31
Rv3236c 3612388 c.729T>G synonymous_variant 0.22
Rv3236c 3612522 p.Ser199Ala missense_variant 0.25
fbiB 3642624 p.Ala364Thr missense_variant 0.17
fbiB 3642744 p.Ala404Ser missense_variant 0.43
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.2
rpoA 3878248 p.Ser87Trp missense_variant 0.22
clpC1 4039890 p.Val272Gly missense_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.27
embC 4240006 c.144A>C synonymous_variant 0.23
embC 4240520 p.Thr220Pro missense_variant 0.3
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240712 p.Trp284Gly missense_variant 0.18
embC 4240715 p.His285Asp missense_variant 0.18
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241412 p.Ile517Thr missense_variant 0.29
embC 4241421 p.Glu520Gly missense_variant 0.25
embC 4241433 p.Met524Arg missense_variant 0.2
embC 4242043 p.Met727Ile missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.25
embC 4242414 p.Leu851Arg missense_variant 0.15
embC 4242422 p.Trp854Gly missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.36
embC 4242908 p.Phe1016Val missense_variant 0.29
embA 4243848 p.Val206Met missense_variant 1.0
embA 4243888 p.Val219Gly missense_variant 0.2
embA 4244619 p.Leu463Val missense_variant 0.22
embA 4244954 c.1722C>T synonymous_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248663 p.Val717Gly missense_variant 0.19
embB 4248689 p.Ile726Val missense_variant 0.44
aftB 4268758 p.Ile27Val missense_variant 0.3
aftB 4268770 p.Gln23Glu missense_variant 0.2
aftB 4268774 p.Ser21Gly missense_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269856 c.-23G>A upstream_gene_variant 0.17
ubiA 4269864 c.-31C>G upstream_gene_variant 0.2
ethR 4327609 p.Ser21Pro missense_variant 0.21
ethR 4327637 p.Leu30Pro missense_variant 0.22
ethR 4327639 p.Ala31Pro missense_variant 0.22
ethR 4327642 p.Thr32Pro missense_variant 0.25
ethR 4327813 p.Thr89Pro missense_variant 0.22
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