TB-Profiler result

Run: SRR6650299
Summary

Run ID: SRR6650299

Sample name:

Date: 15-08-2023 08:22:05

Number of reads: 1423973

Percentage reads mapped: 99.35

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.Ser18* (1.00)
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 2289189 p.Ser18* stop_gained 1.0 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
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 9629 c.2328C>T synonymous_variant 1.0
fgd1 490979 p.Asn66Thr missense_variant 0.27
fgd1 491008 p.Thr76Pro missense_variant 0.31
fgd1 491014 p.Thr78Pro missense_variant 0.36
fgd1 491027 p.Asn82Thr missense_variant 0.34
fgd1 491661 c.879C>G synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575852 p.Trp169Gly missense_variant 0.15
mshA 575856 p.Ala170Gly missense_variant 0.16
mshA 575873 p.Thr176Pro missense_variant 0.22
mshA 575886 p.Leu180Arg missense_variant 0.17
mshA 575926 c.579A>C synonymous_variant 0.17
mshA 576723 p.Val459Gly missense_variant 0.4
ccsA 619707 c.-184T>G upstream_gene_variant 0.22
ccsA 619831 c.-60T>G upstream_gene_variant 0.19
ccsA 620748 c.858T>G synonymous_variant 0.21
ccsA 620770 p.Trp294Arg missense_variant 0.14
rpoB 759610 c.-197T>C upstream_gene_variant 0.2
rpoB 759611 c.-196G>C upstream_gene_variant 0.27
rpoB 759615 c.-192A>C upstream_gene_variant 0.27
rpoB 759620 c.-187A>C upstream_gene_variant 0.19
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
mmpL5 777427 p.Thr352Pro missense_variant 0.19
mmpL5 777572 c.909C>T synonymous_variant 1.0
mmpR5 778226 c.-764T>C upstream_gene_variant 0.19
mmpL5 778239 p.Val81Gly missense_variant 0.19
mmpL5 778252 p.His77Asn missense_variant 0.17
mmpL5 778907 c.-427C>G upstream_gene_variant 0.16
mmpR5 779336 p.Asp116Ala missense_variant 0.29
mmpR5 779346 p.Asp119Glu missense_variant 0.18
mmpR5 779348 p.Val120Gly missense_variant 0.22
mmpR5 779362 p.Leu125Gly missense_variant 0.18
mmpR5 779371 p.Ala128Pro missense_variant 0.22
rpsL 781363 c.-197T>G upstream_gene_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781524 c.-36C>A upstream_gene_variant 0.21
rpsL 781526 c.-34G>A upstream_gene_variant 0.14
rpsL 781536 c.-24G>A upstream_gene_variant 0.16
rplC 800981 p.Ser58Thr missense_variant 0.19
rplC 800988 c.180C>A synonymous_variant 0.15
rplC 800997 p.Asn63Lys missense_variant 0.28
rplC 801019 p.Thr71Pro missense_variant 0.18
rplC 801287 p.Val160Gly missense_variant 0.36
fbiC 1303016 p.Val29Gly missense_variant 0.24
fbiC 1303023 c.93A>G synonymous_variant 0.31
fbiC 1304438 p.Glu503Gly missense_variant 0.2
Rv1258c 1406452 p.Thr297Pro missense_variant 0.2
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461086 c.42A>G synonymous_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473921 n.264A>G non_coding_transcript_exon_variant 0.27
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.14
rrl 1473932 n.275C>A non_coding_transcript_exon_variant 0.19
rrl 1473948 n.291C>A non_coding_transcript_exon_variant 0.14
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.29
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.25
rrl 1473973 n.316T>G non_coding_transcript_exon_variant 0.21
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.5
rrl 1475029 n.1372T>G non_coding_transcript_exon_variant 0.18
rrl 1475066 n.1409C>A non_coding_transcript_exon_variant 0.25
rrl 1476176 n.2519C>G non_coding_transcript_exon_variant 0.19
rrl 1476200 n.2543A>G non_coding_transcript_exon_variant 0.18
fabG1 1673668 p.Glu77Lys missense_variant 0.14
inhA 1673679 c.-523T>G upstream_gene_variant 0.23
fabG1 1673690 p.Val84Gly missense_variant 0.22
fabG1 1674076 p.Thr213Pro missense_variant 0.23
tlyA 1917805 c.-135C>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918044 p.Asp35Glu missense_variant 0.15
tlyA 1918052 p.Pro38Arg missense_variant 0.21
tlyA 1918061 p.Lys41Thr missense_variant 0.15
tlyA 1918066 p.Ala43Pro missense_variant 0.2
tlyA 1918410 c.471C>T synonymous_variant 0.17
ndh 2103222 c.-180A>C upstream_gene_variant 0.19
ndh 2103225 c.-183A>C upstream_gene_variant 0.21
ndh 2103235 c.-193C>G upstream_gene_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155856 p.Thr86Pro missense_variant 0.31
PPE35 2167859 c.2754T>G synonymous_variant 0.26
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169278 c.1335T>G synonymous_variant 0.2
PPE35 2169285 p.Tyr443Phe missense_variant 0.24
PPE35 2169293 c.1320T>G synonymous_variant 0.2
PPE35 2169299 p.Asn438Lys missense_variant 0.2
PPE35 2169308 c.1305C>G synonymous_variant 0.27
PPE35 2169317 c.1296C>T synonymous_variant 0.33
PPE35 2169854 c.759T>G synonymous_variant 0.17
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 0.17
pncA 2289900 c.-659A>C upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.4
kasA 2518151 p.Ser13Arg missense_variant 0.4
kasA 2518605 p.Val164Gly missense_variant 0.36
eis 2715560 c.-228T>G upstream_gene_variant 0.19
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859377 p.Thr348Ala missense_variant 0.33
pepQ 2859438 c.981T>G synonymous_variant 0.19
Rv2752c 3064632 c.1560C>T synonymous_variant 0.96
Rv2752c 3064745 p.Thr483Pro missense_variant 0.18
thyX 3068042 c.-97T>C upstream_gene_variant 0.32
thyA 3073811 p.Ser221Gly missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087909 p.Thr364Pro missense_variant 0.2
fbiD 3339273 c.156T>G synonymous_variant 0.37
fbiD 3339279 c.162T>G synonymous_variant 0.25
fbiD 3339289 p.Ser58Pro missense_variant 0.15
fbiD 3339688 p.Thr191Pro missense_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448819 p.Thr106Pro missense_variant 0.2
Rv3083 3449079 p.Leu192Phe missense_variant 0.29
Rv3083 3449083 p.Pro194Ser missense_variant 0.17
Rv3083 3449107 p.Gly202Arg missense_variant 0.19
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 3611974 c.1143A>C synonymous_variant 0.2
Rv3236c 3612835 c.282T>G synonymous_variant 0.22
fbiB 3642740 c.1206C>T synonymous_variant 0.22
fbiB 3642744 p.Ala404Ser missense_variant 0.29
fbiB 3642751 p.Asp406Ala missense_variant 0.26
fbiB 3642772 p.Asp413Ala missense_variant 0.37
alr 3841253 c.168C>T synonymous_variant 0.97
alr 3841277 c.144C>T synonymous_variant 0.97
alr 3841506 c.-86A>C upstream_gene_variant 0.23
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.33
embC 4240001 p.Thr47Pro missense_variant 0.18
embC 4240006 c.144A>C synonymous_variant 0.19
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.19
embA 4243372 p.Gln47Arg missense_variant 0.18
embA 4243380 p.Thr50Pro missense_variant 0.17
embA 4243398 p.Thr56Pro missense_variant 0.23
embA 4243848 p.Val206Met missense_variant 1.0
embA 4243930 p.Leu233Pro missense_variant 0.16
embA 4244748 p.Thr506Pro missense_variant 0.23
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247623 c.1110G>C synonymous_variant 0.22
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249403 p.Thr964Pro missense_variant 0.2
aftB 4268758 p.Ile27Val missense_variant 0.2
aftB 4268776 p.Ser21Gly missense_variant 0.18
aftB 4268799 p.Val13Gly missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269486 c.-650T>G upstream_gene_variant 0.2
ubiA 4269502 p.Val111Gly missense_variant 0.19
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269848 c.-15A>G upstream_gene_variant 0.23
ubiA 4269864 c.-31C>G upstream_gene_variant 0.24
ethA 4326887 p.Asp196Gly missense_variant 0.21
ethA 4326905 p.Leu190Pro missense_variant 0.17
ethR 4327597 p.Thr17Pro missense_variant 0.2
ethR 4327624 p.Glu26Lys missense_variant 0.18
ethR 4327642 p.Thr32Pro missense_variant 0.42
ethR 4327768 p.Thr74Pro missense_variant 0.18
ethR 4327813 p.Thr89Pro missense_variant 0.23
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