TB-Profiler result

Run: ERR6336757
Summary

Run ID: ERR6336757

Sample name:

Date: 02-04-2023 02:02:18

Number of reads: 1603876

Percentage reads mapped: 98.69

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 7423 p.Leu41Arg missense_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8651 c.1350C>G synonymous_variant 0.11
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9290 c.1989G>A synonymous_variant 0.29
gyrA 9291 c.1990C>T synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9349 p.Phe683Ser missense_variant 0.14
gyrA 9354 p.Ala685Thr missense_variant 0.13
fgd1 490669 c.-113delG upstream_gene_variant 0.2
fgd1 491288 p.Gly169Asp missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575440 c.93C>T synonymous_variant 0.2
mshA 575483 p.Arg46Trp missense_variant 0.14
mshA 575781 p.Pro145Leu missense_variant 0.13
mshA 576100 c.753T>C synonymous_variant 0.2
mshA 576128 c.781C>T synonymous_variant 0.29
mshA 576522 p.Gly392Glu missense_variant 0.4
mshA 576588 p.Gly414Glu missense_variant 0.22
ccsA 619797 c.-94A>G upstream_gene_variant 0.13
rpoB 760439 p.Asp211Glu missense_variant 0.25
rpoB 761152 p.Leu449Gln missense_variant 0.18
rpoB 761162 c.1356G>T synonymous_variant 0.2
rpoB 761617 p.Asn604Thr missense_variant 0.17
rpoB 761649 p.Ser615Arg missense_variant 0.2
rpoB 761701 p.Ala632Val missense_variant 0.23
rpoB 761704 p.Gly633Ala missense_variant 0.14
rpoB 761707 p.Asp634Gly missense_variant 0.14
rpoB 761710 p.Val635Asp missense_variant 0.15
rpoB 761713 p.Val636Asp missense_variant 0.2
rpoB 761719 p.Ala638Val missense_variant 0.15
rpoC 762734 c.-636G>A upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763868 p.Asp167His missense_variant 0.13
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764530 c.1161C>T synonymous_variant 0.18
rpoC 764587 c.1218C>T synonymous_variant 0.22
rpoC 765218 p.Glu617Lys missense_variant 0.13
rpoC 766164 p.Glu932Ala missense_variant 0.12
rpoC 766306 c.2940dupG frameshift_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 777970 p.Thr171Pro missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303607 p.Lys226Thr missense_variant 0.14
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406728 p.Pro205Ala missense_variant 0.12
Rv1258c 1407496 c.-156T>A upstream_gene_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674362 p.Leu54Pro missense_variant 0.33
inhA 1674748 p.Gly183Ser missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102411 p.Val211Ala missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155696 p.Ala139Val missense_variant 0.14
katG 2155803 c.309C>T synonymous_variant 0.13
katG 2156501 c.-390C>G upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288758 p.Gly162Cys missense_variant 0.15
pncA 2290027 c.-786G>T upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518954 c.840C>T synonymous_variant 0.2
kasA 2519044 c.930G>A synonymous_variant 0.5
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519051 p.Thr313Ala missense_variant 0.67
eis 2715469 c.-137T>C upstream_gene_variant 0.17
ahpC 2725994 c.-199G>A upstream_gene_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746411 c.1188G>A synonymous_variant 0.15
folC 2746925 p.Asp225Val missense_variant 0.17
pepQ 2860168 p.Ala84Val missense_variant 0.4
ribD 2987107 p.Ile90Thr missense_variant 0.15
ribD 2987129 c.291G>A synonymous_variant 0.14
ribD 2987530 p.Pro231Leu missense_variant 0.18
thyX 3067307 c.639C>T synonymous_variant 0.22
thyX 3067848 p.Pro33His missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339045 c.-73G>A upstream_gene_variant 0.33
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449238 p.Arg245Ser missense_variant 0.12
fprA 3473842 c.-165G>A upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474095 p.Glu30Val missense_variant 0.13
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474909 c.903A>G synonymous_variant 0.25
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612619 p.Leu166Phe missense_variant 0.2
Rv3236c 3612848 p.Leu90Pro missense_variant 0.11
Rv3236c 3613294 c.-178G>C upstream_gene_variant 0.12
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640609 p.Leu23Phe missense_variant 0.29
fbiA 3641299 p.Arg253Cys missense_variant 0.2
fbiA 3641500 p.Val320Ile missense_variant 0.29
fbiB 3641789 c.255G>A synonymous_variant 0.13
fbiB 3642759 p.Arg409Cys missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 0.12
rpoA 3878639 c.-132C>G upstream_gene_variant 0.38
clpC1 4039086 p.Lys540Thr missense_variant 0.13
clpC1 4039510 p.Ala399Thr missense_variant 0.18
clpC1 4040034 p.Ala224Glu missense_variant 0.18
clpC1 4040181 p.Gly175Val missense_variant 0.14
clpC1 4040247 p.Ala153Val missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240987 c.1125G>T synonymous_variant 0.22
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243735 p.Pro168Leu missense_variant 0.25
embA 4244420 c.1188G>C synonymous_variant 1.0
embB 4245524 c.-990G>A upstream_gene_variant 0.2
embB 4245530 c.-984T>C upstream_gene_variant 0.13
embA 4245786 p.Ala852Thr missense_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246453 p.Val1074Gly missense_variant 0.29
embB 4246460 c.-54G>A upstream_gene_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.2
embB 4246883 p.Asp124Asn missense_variant 0.17
embB 4247578 c.1065G>A synonymous_variant 0.94
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247657 p.Pro382Ser missense_variant 0.33
embB 4247785 c.1272G>A synonymous_variant 0.4
aftB 4267414 p.Gly475Cys missense_variant 0.17
aftB 4268305 p.Val178Leu missense_variant 0.67
aftB 4268445 p.Ala131Gly missense_variant 0.29
aftB 4268530 p.Gly103Ser missense_variant 0.18
aftB 4268847 c.-11C>T upstream_gene_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269564 c.-728G>C upstream_gene_variant 0.13
aftB 4269606 c.-770T>C upstream_gene_variant 0.96
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4269961 c.-128C>T upstream_gene_variant 0.2
ethR 4326808 c.-741G>A upstream_gene_variant 0.12
ethA 4326906 p.Leu190Phe missense_variant 0.14
ethR 4327602 c.55dupC frameshift_variant 0.33
ethR 4328000 p.Ala151Val missense_variant 0.22
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 4408471 c.-269G>A upstream_gene_variant 0.29