TB-Profiler result

Run: ERR9892005
Summary

Run ID: ERR9892005

Sample name:

Date: 02-04-2023 13:27:08

Number of reads: 437252

Percentage reads mapped: 99.6

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 None 0.97
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 2155588 p.Ser175* stop_gained 0.17 isoniazid
embA 4243222 c.-11C>A upstream_gene_variant 0.12 ethambutol
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 6329 p.Glu364* stop_gained 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9286 p.Ala662Val missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 0.2
gyrA 9536 c.2235C>T synonymous_variant 0.2
gyrA 9549 p.Val750Leu missense_variant 0.12
fgd1 490946 p.Leu55Arg missense_variant 0.11
mshA 575521 c.174A>T synonymous_variant 0.17
mshA 576081 p.Asp245Val missense_variant 0.13
mshA 576170 p.Gln275Glu missense_variant 0.18
ccsA 619876 c.-15C>T upstream_gene_variant 0.17
ccsA 620565 c.675G>T synonymous_variant 0.25
rpoB 759921 p.Arg39Ser missense_variant 0.14
rpoB 760163 p.Lys119Asn missense_variant 0.12
rpoB 760350 p.Asp182Tyr missense_variant 0.2
rpoB 761171 c.1365C>A synonymous_variant 0.12
rpoB 761804 p.Met666Ile missense_variant 0.5
rpoC 764419 c.1050C>A synonymous_variant 0.25
rpoC 764625 p.Gly419Asp missense_variant 0.11
rpoC 766347 p.Glu993Gly missense_variant 0.18
rpoC 767042 p.Ser1225Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775675 c.2805delG frameshift_variant 0.5
mmpL5 776334 p.Val716Ala missense_variant 0.15
mmpL5 776393 c.2088C>T synonymous_variant 0.17
mmpL5 776618 c.1863G>A synonymous_variant 0.14
mmpL5 777305 c.1176C>A synonymous_variant 0.18
mmpL5 777468 p.Pro338Leu missense_variant 0.18
mmpS5 778722 p.Gly62Cys missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781397 c.-163G>T upstream_gene_variant 0.2
rpsL 781413 c.-147T>A upstream_gene_variant 0.17
rpsL 781482 c.-78A>T upstream_gene_variant 0.18
rplC 801007 p.Thr67Ser missense_variant 0.12
fbiC 1303384 p.Glu152Lys missense_variant 0.12
fbiC 1303683 c.753G>A synonymous_variant 0.25
fbiC 1305403 p.Gly825Arg missense_variant 0.13
Rv1258c 1406310 p.Leu344Pro missense_variant 0.11
Rv1258c 1406639 c.702C>A synonymous_variant 0.15
Rv1258c 1407115 p.Met76Leu missense_variant 0.17
embR 1416669 p.Ala227Ser missense_variant 0.11
embR 1417490 c.-143C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
rrl 1474379 n.722G>T non_coding_transcript_exon_variant 0.11
fabG1 1673771 p.Ala111Asp missense_variant 0.13
inhA 1674615 p.Met138Ile missense_variant 0.15
inhA 1674616 p.Asn139Tyr missense_variant 0.15
inhA 1674785 p.Arg195Pro missense_variant 0.15
inhA 1674816 c.615T>A synonymous_variant 0.18
rpsA 1833363 c.-179A>T upstream_gene_variant 0.33
rpsA 1833528 c.-14A>G upstream_gene_variant 0.17
rpsA 1833701 p.Asp54Asn missense_variant 0.12
rpsA 1833972 c.435_436delCG frameshift_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918395 c.456G>T synonymous_variant 0.12
ndh 2102047 c.996G>T synonymous_variant 0.13
ndh 2103002 p.Arg14Met missense_variant 0.13
katG 2153903 p.Phe737Leu missense_variant 0.11
katG 2154149 p.Asn655Tyr missense_variant 0.12
katG 2154167 p.Ala649Ser missense_variant 0.15
katG 2154588 p.Asn508Lys missense_variant 0.12
katG 2154676 p.Ala479Val missense_variant 0.22
katG 2155296 c.816C>T synonymous_variant 0.12
katG 2155528 p.Glu195Val missense_variant 0.29
PPE35 2167724 c.2889G>T synonymous_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.1
PPE35 2169269 c.1344A>G synonymous_variant 0.11
PPE35 2169272 c.1341C>G synonymous_variant 0.11
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169293 c.1320T>C synonymous_variant 0.13
PPE35 2169447 p.Phe389Ser missense_variant 0.1
PPE35 2169517 p.Ser366Pro missense_variant 0.11
PPE35 2169592 p.Ile341Phe missense_variant 0.14
PPE35 2169962 c.651C>A synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170236 p.Phe126Tyr missense_variant 0.29
Rv1979c 2222021 c.1144C>A synonymous_variant 0.14
Rv1979c 2223287 c.-123G>T upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290041 c.-800C>A upstream_gene_variant 0.12
kasA 2518435 c.321G>T synonymous_variant 0.11
ahpC 2726155 c.-38A>T upstream_gene_variant 0.15
folC 2746489 p.Phe370Leu missense_variant 0.4
folC 2747055 p.Asp182Tyr missense_variant 0.18
folC 2747087 p.Ala171Glu missense_variant 0.13
pepQ 2860173 p.Tyr82* stop_gained 0.14
ribD 2986804 c.-34delG upstream_gene_variant 0.14
ribD 2987162 c.324C>T synonymous_variant 0.25
ribD 2987496 p.Val220Phe missense_variant 0.18
ribD 2987582 c.744C>A synonymous_variant 0.17
Rv2752c 3064598 p.Gly532Trp missense_variant 0.14
Rv2752c 3064846 p.Val449Ala missense_variant 0.17
Rv2752c 3065555 p.Pro213Thr missense_variant 0.14
Rv2752c 3065711 p.Gly161Cys missense_variant 0.29
Rv2752c 3065775 c.417T>C synonymous_variant 0.22
ald 3087263 p.His148Gln missense_variant 1.0
fbiD 3339670 c.553C>T synonymous_variant 0.13
Rv3083 3449033 p.Gly177Asp missense_variant 0.13
Rv3083 3449333 p.Leu277Arg missense_variant 0.11
Rv3083 3449674 p.Thr391Ala missense_variant 0.12
Rv3083 3449709 c.1206C>G synonymous_variant 0.14
fprA 3474221 p.Glu72Gly missense_variant 0.12
fprA 3474932 p.Glu309Val missense_variant 0.17
whiB7 3568648 p.Pro11Leu missense_variant 0.12
fbiB 3641259 c.-276G>T upstream_gene_variant 0.22
fbiB 3642008 c.474C>T synonymous_variant 0.12
alr 3840371 c.1050G>T synonymous_variant 0.11
alr 3841029 p.Ala131Val missense_variant 0.14
alr 3841464 c.-44C>A upstream_gene_variant 0.11
ddn 3986708 c.-136C>T upstream_gene_variant 0.12
clpC1 4038282 p.Asp808Gly missense_variant 0.15
clpC1 4038695 c.2010C>T synonymous_variant 0.15
clpC1 4038962 c.1743C>T synonymous_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.17
embC 4240020 c.160delC frameshift_variant 0.14
embC 4240377 p.Val172Ala missense_variant 0.11
embC 4240644 p.Arg261Leu missense_variant 0.29
embC 4241266 c.1404C>T synonymous_variant 0.17
embC 4241372 p.Arg504Ser missense_variant 0.11
embC 4241384 p.Pro508Thr missense_variant 0.13
embC 4241921 p.Gly687Trp missense_variant 0.29
embC 4242059 p.Ala733Ser missense_variant 0.12
embC 4242345 p.Ala828Asp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243056 p.Pro1065Leu missense_variant 0.13
embA 4243066 c.-167C>T upstream_gene_variant 0.13
embA 4243275 p.Leu15Ile missense_variant 0.14
embA 4243315 p.Cys28Phe missense_variant 0.17
embA 4244225 c.993C>T synonymous_variant 0.17
embA 4244696 p.Lys488Asn missense_variant 1.0
embA 4245209 p.Leu659Phe missense_variant 0.13
embB 4245686 c.-828G>T upstream_gene_variant 0.33
embB 4247621 p.Leu370Met missense_variant 0.2
embB 4247658 p.Pro382His missense_variant 0.25
embB 4247980 c.1467C>A synonymous_variant 0.12
embB 4248435 p.Ala641Asp missense_variant 0.14
embB 4249732 c.3219C>G synonymous_variant 1.0
embB 4249787 p.Gly1092Cys missense_variant 0.13
aftB 4267121 c.1716G>C synonymous_variant 0.12
aftB 4267654 p.Met395Val missense_variant 0.18
aftB 4268388 p.Leu150Pro missense_variant 0.14
ethA 4326012 p.Gly488Trp missense_variant 0.11
ethA 4326712 p.Gln254His missense_variant 0.15
ethA 4328133 c.-660C>T upstream_gene_variant 0.12
whiB6 4338564 c.-43C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407614 p.Arg197Ser missense_variant 0.22