TB-Profiler result

Run: ERR233365
Summary

Run ID: ERR233365

Sample name:

Date: 27-03-2023 08:27:35

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage1.1.1.1

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
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
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 1.0
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO 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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.19
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.498A>C synonymous_variant 0.17
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 490696 c.-87T>G upstream_gene_variant 0.16
fgd1 490972 p.Arg64Ser missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575932 p.Glu195Asp missense_variant 0.23
ccsA 620407 p.Pro173Ala missense_variant 0.24
rpoB 759831 p.Thr9Pro missense_variant 0.17
rpoB 761285 c.1479G>C synonymous_variant 0.17
rpoC 762836 c.-534C>G 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 764725 p.Phe452Leu missense_variant 0.17
rpoC 764905 p.Phe512Leu missense_variant 0.18
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406358 p.Ile328Thr missense_variant 0.17
Rv1258c 1407240 p.Val34Gly missense_variant 0.2
embR 1417019 p.Cys110Tyr missense_variant 0.97
embR 1417136 p.Ser71Ile missense_variant 0.13
rrs 1471658 n.-188T>G upstream_gene_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.21
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.13
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.14
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.17
inhA 1674892 p.Asn231Asp missense_variant 0.24
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.27
ndh 2102891 p.Phe51Ser missense_variant 0.24
katG 2154036 p.Ser692Arg missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169379 p.Phe412Val missense_variant 0.16
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290023 c.-782A>C upstream_gene_variant 0.38
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518891 c.777C>A synonymous_variant 0.18
eis 2714355 c.978C>G synonymous_variant 0.21
eis 2714366 p.Val323Leu missense_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726737 p.Asp182Ala missense_variant 0.14
ahpC 2726756 c.564C>G synonymous_variant 0.22
pepQ 2859381 c.1038C>G synonymous_variant 0.15
ribD 2987392 p.Arg185Pro missense_variant 0.23
Rv2752c 3064552 p.Arg547Pro missense_variant 0.11
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064741 p.Gly484Ala missense_variant 0.19
Rv2752c 3065618 p.Gly192Arg missense_variant 0.16
thyA 3073890 p.Leu194Phe missense_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339550 p.Gly145Trp missense_variant 0.21
Rv3083 3448714 p.Asp71His missense_variant 0.98
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 0.26
fbiB 3641873 c.339C>T synonymous_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.14
alr 3840268 p.Thr385Pro missense_variant 0.17
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4039363 p.Ala448Pro missense_variant 0.28
clpC1 4039680 p.Phe342Ser missense_variant 0.21
clpC1 4039931 p.Gly258Val missense_variant 0.21
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240355 p.Ala165Pro missense_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.19
embC 4241456 p.Ala532Pro missense_variant 0.38
embC 4241783 p.Trp641Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.19
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246423 p.Val1064Gly missense_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248725 p.Ser738Ala missense_variant 0.17
aftB 4267156 p.Gln561Lys missense_variant 0.19
aftB 4267165 p.Trp558Gly missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269525 c.-689C>T upstream_gene_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.14
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0