TB-Profiler result

Run: ERR6336754
Summary

Run ID: ERR6336754

Sample name:

Date: 02-04-2023 02:02:12

Number of reads: 1734956

Percentage reads mapped: 99.05

Strain: lineage1.2.1.2.1

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 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 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
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 7416 c.116delG frameshift_variant 0.11
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 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490895 p.Ser38Ile missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575866 p.Leu173Phe missense_variant 0.17
mshA 576537 p.Gln397Pro missense_variant 0.1
ccsA 619752 c.-139A>C upstream_gene_variant 0.14
rpoB 761152 p.Leu449Gln missense_variant 0.15
rpoB 762278 c.2472C>T synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763927 c.558C>T synonymous_variant 0.5
rpoC 765153 p.Asp595Ala missense_variant 0.11
rpoC 765164 p.Tyr599His missense_variant 0.12
rpoC 767026 c.3657G>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777277 p.Leu402Phe missense_variant 0.15
mmpR5 779369 p.Asp127Gly missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801215 p.Gly136Ala missense_variant 0.12
rplC 801242 p.His145Pro missense_variant 0.2
fbiC 1303910 p.Pro327Leu missense_variant 0.14
fbiC 1303961 p.Arg344Pro missense_variant 0.25
fbiC 1304070 c.1140C>G synonymous_variant 0.13
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1416526 c.822C>G synonymous_variant 0.11
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417053 p.Pro99Ser missense_variant 0.17
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673564 p.Val42Glu missense_variant 0.4
fabG1 1673635 p.Asp66Asn missense_variant 0.14
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674416 p.Ala72Val missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918542 c.603G>C synonymous_variant 0.2
tlyA 1918610 p.Gly224Asp missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155392 c.720C>T synonymous_variant 0.12
katG 2155909 p.Val68Ala missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170145 c.468C>T synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289454 c.-213A>G upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519054 p.Ala314Thr missense_variant 0.13
eis 2714892 c.441G>A synonymous_variant 0.22
eis 2714913 c.420G>C synonymous_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746182 c.1416delT frameshift_variant 0.12
folC 2747156 p.Ala148Val missense_variant 0.12
folC 2747415 p.Arg62Cys missense_variant 0.12
folC 2747664 c.-66C>T upstream_gene_variant 0.17
folC 2747721 c.-123C>T upstream_gene_variant 0.13
thyX 3067285 p.Ala221Thr missense_variant 0.13
thyX 3067538 c.408C>T synonymous_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087249 p.Val144Ile missense_variant 0.14
ald 3087263 p.His148Gln missense_variant 0.17
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448853 p.Thr117Asn missense_variant 0.12
Rv3083 3449773 p.Arg424Cys missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474637 p.Glu211Lys missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475323 c.1317T>C synonymous_variant 0.17
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612155 p.Arg321Pro missense_variant 0.12
Rv3236c 3612563 p.Met185Thr missense_variant 0.17
Rv3236c 3612575 p.Ala181Val missense_variant 0.12
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3641610 p.Gly26Ser missense_variant 0.13
fbiB 3642759 p.Arg409Cys missense_variant 1.0
alr 3840997 p.Leu142Met missense_variant 0.12
rpoA 3878567 c.-60C>G upstream_gene_variant 0.43
rpoA 3878639 c.-132C>G upstream_gene_variant 0.16
ddn 3987029 c.186C>T synonymous_variant 0.11
clpC1 4039567 p.Val380Leu missense_variant 0.17
clpC1 4040268 p.Gln146Arg missense_variant 0.2
clpC1 4040276 c.429C>T synonymous_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239886 c.24C>A synonymous_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241025 p.Val388Ala missense_variant 0.17
embC 4241036 p.Leu392Phe missense_variant 0.18
embC 4241039 p.Asp393Asn missense_variant 0.18
embC 4241042 p.Asn394Asp missense_variant 0.82
embC 4241050 c.1188T>G synonymous_variant 0.14
embC 4241053 c.1191G>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243176 c.-57A>G upstream_gene_variant 0.14
embA 4243192 c.-41A>C upstream_gene_variant 0.13
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243926 p.Thr232Ala missense_variant 0.14
embA 4243954 c.725delC frameshift_variant 0.2
embA 4244194 p.Gly321Ala missense_variant 0.13
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245694 p.Ile821Thr missense_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246563 p.Leu17Trp missense_variant 0.23
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267567 c.1270C>T synonymous_variant 0.15
aftB 4267593 p.Ala415Val missense_variant 0.12
aftB 4268889 c.-53C>T upstream_gene_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4270011 c.-178A>G upstream_gene_variant 0.12
ubiA 4270016 c.-183G>A upstream_gene_variant 0.12
ethR 4326841 c.-708G>A upstream_gene_variant 0.15
whiB6 4338348 c.174C>T synonymous_variant 1.0
whiB6 4338361 p.Arg54Gln 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
gid 4408226 c.-24C>T upstream_gene_variant 1.0
gid 4408474 c.-272A>T upstream_gene_variant 0.13