TB-Profiler result

Run: ERR9893571
Summary

Run ID: ERR9893571

Sample name:

Date: 02-04-2023 13:27:27

Number of reads: 440174

Percentage reads mapped: 98.21

Strain:

Drug-resistance: HR-TB

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7526 c.225G>A synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7814 c.513C>A synonymous_variant 0.2
gyrA 8457 p.Glu386* stop_gained 0.12
gyrA 8761 p.Val487Ala missense_variant 0.17
gyrA 8781 c.1480C>A synonymous_variant 0.2
gyrA 9137 c.1836C>A synonymous_variant 0.33
gyrA 9183 p.Arg628Ser missense_variant 0.18
gyrA 9192 c.1891C>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9313 p.Leu671Pro missense_variant 0.15
fgd1 490718 c.-65G>T upstream_gene_variant 0.33
mshA 576529 p.Glu394Asp missense_variant 0.5
mshA 576596 p.Met417Leu missense_variant 0.5
ccsA 619785 c.-106G>C upstream_gene_variant 1.0
ccsA 620480 p.Leu197Pro missense_variant 0.29
ccsA 620724 c.834C>T synonymous_variant 0.4
ccsA 620817 c.927C>T synonymous_variant 0.18
rpoB 759615 c.-192A>C upstream_gene_variant 0.27
rpoB 760415 c.609C>A synonymous_variant 0.11
rpoB 760589 c.783C>A synonymous_variant 0.33
rpoB 760646 c.840C>A synonymous_variant 0.25
rpoB 760681 p.Asn292Ser missense_variant 0.33
rpoB 760988 c.1182C>A synonymous_variant 0.22
rpoB 761031 p.Gln409Lys missense_variant 0.29
rpoB 762039 p.His745Asn missense_variant 0.18
rpoB 762413 p.Gln869His missense_variant 0.2
rpoC 763491 p.Pro41Arg missense_variant 0.25
rpoC 763609 c.240C>A synonymous_variant 0.18
rpoC 763676 p.His103Asn missense_variant 1.0
rpoC 764230 p.Gln287His missense_variant 0.29
rpoC 764484 p.Arg372Leu missense_variant 0.12
rpoC 764516 p.Asp383Tyr missense_variant 0.13
rpoC 764890 p.Leu507Phe missense_variant 0.15
rpoC 767092 c.3723C>A synonymous_variant 1.0
mmpL5 776393 c.2088C>T synonymous_variant 0.15
mmpL5 776709 p.Cys591Tyr missense_variant 0.5
mmpL5 776789 c.1692C>A synonymous_variant 1.0
mmpL5 777019 p.Asp488Tyr missense_variant 0.25
mmpL5 777100 p.Asp461Tyr missense_variant 0.22
mmpL5 778002 p.Ser160* stop_gained 0.13
mmpS5 778622 p.Thr95Met missense_variant 0.18
mmpS5 779567 c.-662G>T upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781525 c.-35A>G upstream_gene_variant 0.17
rpsL 781571 c.12C>A synonymous_variant 0.12
rpsL 781873 p.Gln105Arg missense_variant 0.33
rplC 801411 c.604delA frameshift_variant 0.25
fbiC 1303432 p.Asp168Tyr missense_variant 0.17
fbiC 1304124 p.Tyr398* stop_gained 0.22
fbiC 1304571 c.1641G>T synonymous_variant 0.2
Rv1258c 1407117 p.Ser75* stop_gained 0.29
Rv1258c 1407310 p.Leu11Met missense_variant 0.14
embR 1416303 p.Gly349Cys missense_variant 0.14
embR 1416308 p.Ser347Tyr missense_variant 0.12
embR 1416497 p.Ser284Leu missense_variant 0.25
embR 1416822 p.Ala176Ser missense_variant 0.29
embR 1416889 c.459G>T synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833691 p.Glu50Asp missense_variant 0.18
rpsA 1833886 c.345C>A synonymous_variant 0.17
rpsA 1834074 p.Lys178Met missense_variant 0.18
rpsA 1834168 c.627C>A synonymous_variant 0.18
rpsA 1834230 p.Gly230Val missense_variant 0.17
rpsA 1834241 p.Leu234Met missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918341 c.402C>A synonymous_variant 1.0
tlyA 1918399 p.Asp154Tyr missense_variant 0.33
ndh 2102438 p.Arg202Leu missense_variant 0.22
ndh 2102854 c.189C>A synonymous_variant 0.5
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154231 c.1881G>T synonymous_variant 0.25
katG 2155008 p.Phe368Leu missense_variant 0.22
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289227 c.15C>A synonymous_variant 0.22
pncA 2289505 c.-264G>T upstream_gene_variant 0.29
kasA 2518333 c.219C>A synonymous_variant 0.18
kasA 2518431 p.Asp106Gly missense_variant 0.17
kasA 2518962 p.Asp283Gly missense_variant 0.18
kasA 2519249 p.Glu379* stop_gained 0.2
folC 2746214 p.Ser462Leu missense_variant 0.29
folC 2746327 c.1272G>T synonymous_variant 0.67
folC 2746906 c.693C>A synonymous_variant 0.33
pepQ 2860251 c.168C>T synonymous_variant 1.0
Rv2752c 3064530 c.1662G>A synonymous_variant 0.33
Rv2752c 3064802 p.Glu464* stop_gained 0.29
Rv2752c 3065032 p.Gly387Val missense_variant 0.13
Rv2752c 3065072 p.Gly374Cys missense_variant 0.18
Rv2752c 3065460 c.732G>T synonymous_variant 0.13
Rv2752c 3065484 c.708G>T synonymous_variant 0.25
Rv2752c 3066131 p.Leu21Met missense_variant 0.2
Rv2752c 3067041 c.-850C>A upstream_gene_variant 0.5
thyX 3067318 p.Arg210* stop_gained 0.5
thyX 3067783 p.Ala55Ser missense_variant 0.33
thyA 3073853 p.His207Asn missense_variant 0.2
thyA 3074481 c.-10C>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086994 p.Gly59Cys missense_variant 0.18
ald 3087081 p.Gly88Trp missense_variant 0.17
ald 3087650 c.831C>A synonymous_variant 0.12
ald 3087655 p.Arg279Leu missense_variant 0.12
ald 3087675 p.Pro286Thr missense_variant 0.12
fbiD 3339145 p.Ile10Val missense_variant 0.25
fbiD 3339688 p.Thr191Pro missense_variant 0.4
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448854 c.351C>A synonymous_variant 0.17
Rv3083 3449327 p.Arg275Leu missense_variant 0.29
Rv3083 3449479 p.Glu326Gln missense_variant 0.33
Rv3083 3449745 c.1242C>A synonymous_variant 0.12
Rv3083 3449934 c.1431C>A synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474191 p.Ser62* stop_gained 0.4
fprA 3474636 c.630G>A synonymous_variant 0.4
fprA 3474764 p.Arg253His missense_variant 0.18
fprA 3474800 p.Arg265Leu missense_variant 0.22
fprA 3474919 p.Lys305Gln missense_variant 0.5
fprA 3474922 p.Asp306His missense_variant 0.5
fprA 3475195 p.Ser397Arg missense_variant 1.0
whiB7 3568569 p.Glu37Asp missense_variant 0.25
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3613181 c.-65C>A upstream_gene_variant 0.15
fbiA 3640409 c.-134C>A upstream_gene_variant 0.25
fbiB 3640956 c.-579G>T upstream_gene_variant 0.22
fbiB 3641936 c.402C>A synonymous_variant 0.2
fbiB 3642468 p.Arg312Trp missense_variant 0.5
alr 3840751 p.Glu224* stop_gained 0.17
alr 3841471 c.-51A>C upstream_gene_variant 0.2
alr 3841608 c.-188A>G upstream_gene_variant 1.0
rpoA 3877607 p.Leu301Met missense_variant 0.33
rpoA 3877688 p.Glu274* stop_gained 0.2
rpoA 3877719 p.Cys263* stop_gained 0.17
rpoA 3877785 c.723C>T synonymous_variant 0.2
rpoA 3878037 c.471C>A synonymous_variant 0.22
rpoA 3878120 p.Asp130Tyr missense_variant 0.2
rpoA 3878408 p.Leu34Met missense_variant 0.14
ddn 3987106 p.Trp88Leu missense_variant 0.17
clpC1 4040522 c.183T>C synonymous_variant 1.0
clpC1 4040583 p.Gly41Val missense_variant 0.2
clpC1 4040665 p.Val14Ile missense_variant 1.0
embC 4240174 c.312G>T synonymous_variant 0.6
embC 4240414 c.552G>T synonymous_variant 0.5
embC 4241542 c.1680C>T synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244639 c.1407G>T synonymous_variant 0.22
embA 4245234 p.Met668Leu missense_variant 0.17
embA 4245405 p.Ala725Ser missense_variant 0.5
embA 4245579 p.Ser783Pro missense_variant 1.0
embB 4246918 c.405G>A synonymous_variant 0.5
embB 4247134 c.621C>T synonymous_variant 0.25
embB 4249646 c.3133C>A synonymous_variant 1.0
aftB 4267309 p.Leu510Met missense_variant 0.67
aftB 4267568 c.1269G>T synonymous_variant 0.33
aftB 4268041 c.796C>T synonymous_variant 1.0
aftB 4268622 p.Trp72Leu missense_variant 1.0
ubiA 4269757 p.Trp26Leu missense_variant 0.4
ethA 4326005 c.1469A>C stop_lost&splice_region_variant 1.0
ethA 4326019 c.1455C>T synonymous_variant 1.0
ethA 4326208 c.1266G>T synonymous_variant 0.13
ethR 4327153 c.-396G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338695 c.-174G>T upstream_gene_variant 0.25
gid 4407645 c.558C>A synonymous_variant 0.13
gid 4407665 p.Ala180Thr missense_variant 0.13
gid 4407846 c.357C>G synonymous_variant 0.18
gid 4408175 p.Ala10Ser missense_variant 0.17
gid 4408463 c.-261C>A upstream_gene_variant 0.22