TB-Profiler result

Run: ERR6336802
Summary

Run ID: ERR6336802

Sample name:

Date: 02-04-2023 02:03:57

Number of reads: 623876

Percentage reads mapped: 99.32

Strain: lineage1.2.1.2

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
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
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
ethA 4327363 c.110delA frameshift_variant 0.2 ethionamide, ethionamide
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 5133 c.-107A>C upstream_gene_variant 0.13
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6459 p.Val407Glu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7751 c.450C>T synonymous_variant 0.12
gyrA 8228 c.927G>A synonymous_variant 0.14
gyrA 8255 c.954C>A synonymous_variant 0.15
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
gyrA 9338 c.2037G>A synonymous_variant 0.12
fgd1 491348 p.Gly189Ala missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575162 c.-186T>C upstream_gene_variant 0.14
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575863 c.516G>A synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.5
rpoB 762640 p.Gly945Glu missense_variant 1.0
rpoB 762847 p.Pro1014Leu missense_variant 0.12
rpoB 762898 p.Val1031Ala missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763674 p.Thr102Ser missense_variant 0.11
rpoC 763831 c.462A>G synonymous_variant 0.11
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776983 c.1498C>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801067 p.Asp87Asn missense_variant 0.12
fbiC 1302870 c.-61G>A upstream_gene_variant 0.18
fbiC 1304459 c.1530_1531delCG frameshift_variant 0.15
Rv1258c 1406198 c.1143C>T synonymous_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417320 p.Arg10Trp missense_variant 0.15
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472672 n.827G>A non_coding_transcript_exon_variant 0.12
rrs 1472762 n.917C>T non_coding_transcript_exon_variant 0.12
rrl 1473521 n.-136delT upstream_gene_variant 0.15
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 1.0
rrl 1476047 n.2390G>A non_coding_transcript_exon_variant 0.12
inhA 1674788 p.Thr196Met missense_variant 0.17
rpsA 1833591 p.Gly17Asp missense_variant 0.17
rpsA 1833897 p.Leu119Pro missense_variant 0.12
tlyA 1917817 c.-123A>C upstream_gene_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102606 p.Glu146Gly missense_variant 0.18
ndh 2102868 p.Ala59Thr missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154850 p.Gly421Asp missense_variant 0.18
PPE35 2167688 c.2925C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168087 c.2526G>A synonymous_variant 0.13
PPE35 2168292 p.Leu774Ser missense_variant 0.11
PPE35 2169571 p.Ser348Gly missense_variant 0.11
Rv1979c 2222308 p.Asp286Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288692 p.Cys184Arg missense_variant 0.15
pncA 2288914 p.Asp110Asn missense_variant 0.17
pncA 2288994 p.Pro83Leu missense_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519078 p.Glu322Lys missense_variant 0.14
eis 2714349 c.984G>A synonymous_variant 0.25
eis 2714445 c.888G>A synonymous_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747762 c.-164G>A upstream_gene_variant 0.12
pepQ 2859438 c.981T>C synonymous_variant 0.1
Rv2752c 3066016 p.Leu59Gln missense_variant 0.12
thyA 3074005 p.Asp156Ala missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087464 c.645C>T synonymous_variant 0.18
fbiD 3339040 c.-78T>C upstream_gene_variant 0.22
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339741 c.624G>T synonymous_variant 0.29
fbiD 3339744 c.627A>C synonymous_variant 0.29
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449096 p.Gly198Asp missense_variant 0.2
fprA 3473819 c.-188A>C upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474908 p.Arg301Gln missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612138 p.Gly327Ser missense_variant 0.14
Rv3236c 3612413 p.Ser235Trp missense_variant 0.2
Rv3236c 3612592 p.Asp175Glu missense_variant 0.13
Rv3236c 3613025 p.Ser31Leu missense_variant 0.2
Rv3236c 3613239 c.-123A>T upstream_gene_variant 0.18
Rv3236c 3613299 c.-183C>T upstream_gene_variant 0.2
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3641347 p.Ala269Thr missense_variant 0.22
fbiB 3642592 p.Val353Gly missense_variant 0.12
alr 3840527 c.894A>G synonymous_variant 0.13
alr 3841516 c.-96G>A upstream_gene_variant 0.12
rpoA 3878329 p.Leu60Gln missense_variant 0.13
clpC1 4038271 p.Pro812Ser missense_variant 0.12
clpC1 4038789 p.Leu639Pro missense_variant 0.12
clpC1 4040173 p.Leu178Phe missense_variant 0.15
clpC1 4040222 c.483G>A synonymous_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040708 c.-4A>G upstream_gene_variant 0.11
panD 4044082 p.Gly67Asp missense_variant 0.12
embC 4240026 p.Thr55Ile missense_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242170 p.Thr770Ala missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242933 p.Val1024Glu missense_variant 0.15
embC 4243083 p.Asp1074Ala missense_variant 0.11
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244184 p.Ser318Gly missense_variant 0.12
embA 4244212 p.Pro327Arg missense_variant 0.11
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246563 p.Leu17Trp missense_variant 0.75
embB 4246567 c.54G>T synonymous_variant 0.6
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4247033 p.Ser174Cys missense_variant 0.4
embB 4247236 c.723G>A synonymous_variant 0.15
embB 4247252 p.Ser247Pro missense_variant 0.17
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248437 p.Thr642Ala missense_variant 0.11
embB 4249744 c.3231G>A synonymous_variant 0.17
embB 4249751 c.3238T>C synonymous_variant 0.14
aftB 4267846 p.Gly331Ser missense_variant 0.15
aftB 4268576 c.261C>A synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326045 p.Gly477Ser missense_variant 0.12
ethR 4327441 c.-108G>A upstream_gene_variant 0.5
ethA 4328157 c.-684C>G upstream_gene_variant 0.18
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 4407700 p.His168Arg missense_variant 0.12
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407958 p.Ala82Val missense_variant 0.15
gid 4408092 c.111A>C synonymous_variant 0.29
gid 4408099 p.Leu35Arg missense_variant 0.29
gid 4408113 c.90T>G synonymous_variant 0.4