TB-Profiler result

Run: ERR11465189

Summary

Run ID: ERR11465189

Sample name:

Date: 07-01-2024 14:47:12

Number of reads: 2027251

Percentage reads mapped: 99.83

Strain: lineage4.9.1

Drug-resistance: RR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser431Thr (0.12)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
lineage4.9.1 Euro-American (H37Rv-like) T1 None 0.99
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
rpoB 761098 p.Ser431Thr missense_variant 0.12 rifampicin
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 6362 c.-940T>C upstream_gene_variant 0.14
gyrA 6793 c.-509T>C upstream_gene_variant 0.15
gyrB 6797 p.Gly520Ser missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7427 c.126G>C synonymous_variant 0.18
gyrA 7430 p.Glu43Asp missense_variant 0.18
gyrA 8354 c.1053G>C synonymous_variant 0.15
gyrA 8570 p.Glu423Asp missense_variant 0.15
gyrA 8579 p.Asp426Glu missense_variant 0.17
gyrA 8580 p.Ile427Val missense_variant 0.17
gyrA 8783 c.1482G>T synonymous_variant 0.16
gyrA 8818 p.Ser506Thr missense_variant 0.17
gyrA 8828 c.1527T>C synonymous_variant 0.16
gyrA 8829 c.1528_1530delTTGinsCTC synonymous_variant 0.16
gyrA 8978 c.1677C>T synonymous_variant 0.98
fgd1 491013 c.231C>G synonymous_variant 0.13
rpoB 760172 c.366G>C synonymous_variant 0.24
rpoB 760181 c.375T>G synonymous_variant 0.16
rpoB 760184 c.378A>G synonymous_variant 0.15
rpoB 760235 c.429T>C synonymous_variant 0.16
rpoB 760244 c.438G>C synonymous_variant 0.17
rpoB 760256 c.450C>T synonymous_variant 0.19
rpoB 760274 p.Glu156Asp missense_variant 0.13
rpoB 760430 c.624T>C synonymous_variant 0.21
rpoB 760433 c.627C>T synonymous_variant 0.21
rpoB 760460 c.654G>C synonymous_variant 0.12
rpoB 760502 c.696C>G synonymous_variant 0.14
rpoB 760591 p.Val262Ala missense_variant 0.16
rpoB 760611 c.805_807delTTGinsCTC synonymous_variant 0.27
rpoB 760634 c.828T>C synonymous_variant 0.13
rpoB 760982 c.1176G>C synonymous_variant 0.13
rpoB 761015 c.1209G>C synonymous_variant 0.15
rpoB 761021 c.1215G>C synonymous_variant 0.14
rpoB 761051 c.1245G>C synonymous_variant 0.13
rpoB 761057 c.1251G>C synonymous_variant 0.14
rpoB 761084 c.1278C>A synonymous_variant 0.12
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.13
rpoB 761102 c.1296A>G synonymous_variant 0.12
rpoB 761132 c.1326G>T synonymous_variant 0.17
rpoB 761133 c.1327T>C synonymous_variant 0.18
rpoB 761147 c.1341C>T synonymous_variant 0.16
rpoB 761150 c.1344A>T synonymous_variant 0.15
rpoB 761234 c.1428G>C synonymous_variant 0.16
rpoB 761249 c.1443A>G synonymous_variant 0.19
rpoB 761273 c.1467T>C synonymous_variant 0.18
rpoB 761282 c.1476C>T synonymous_variant 0.17
rpoB 761318 c.1512G>C synonymous_variant 0.15
rpoB 761327 c.1521A>G synonymous_variant 0.2
rpoB 761573 c.1767C>G synonymous_variant 0.17
rpoB 761579 c.1773G>C synonymous_variant 0.22
rpoB 761972 c.2166C>T synonymous_variant 0.15
rpoB 762053 c.2247T>C synonymous_variant 0.13
rpoB 762062 c.2256T>C synonymous_variant 0.14
rpoB 762065 c.2259T>C synonymous_variant 0.14
rpoB 762080 c.2274G>C synonymous_variant 0.16
rpoB 762086 c.2280G>C synonymous_variant 0.19
rpoB 762101 c.2295C>G synonymous_variant 0.17
rpoB 762114 p.Ile770Val missense_variant 0.15
rpoB 762119 c.2313C>G synonymous_variant 0.14
rpoB 762218 c.2412T>C synonymous_variant 0.15
rpoB 762233 c.2427G>C synonymous_variant 0.15
rpoB 762245 c.2439G>C synonymous_variant 0.14
rpoB 762254 c.2448T>C synonymous_variant 0.16
rpoB 762257 c.2451C>G synonymous_variant 0.16
rpoB 762284 c.2478G>C synonymous_variant 0.12
rpoB 762293 c.2487T>G synonymous_variant 0.12
rpoB 762296 c.2490G>C synonymous_variant 0.2
rpoB 762299 c.2493G>C synonymous_variant 0.19
rpoB 762881 p.Met1025Ile missense_variant 0.19
rpoC 762899 c.-471G>C upstream_gene_variant 0.26
rpoC 763013 c.-357C>G upstream_gene_variant 0.15
rpoC 763053 c.-317_-315delTTGinsCTC upstream_gene_variant 0.15
rpoC 763088 c.-282C>G upstream_gene_variant 0.18
rpoC 763115 c.-255T>C upstream_gene_variant 0.13
rpoC 763127 c.-243G>C upstream_gene_variant 0.16
rpoC 763148 c.-222G>C upstream_gene_variant 0.13
rpoC 763444 c.75T>C synonymous_variant 0.12
rpoC 763456 c.87A>G synonymous_variant 0.16
rpoC 763546 c.177A>G synonymous_variant 0.13
rpoC 763558 c.189C>T synonymous_variant 0.14
rpoC 763570 c.201G>T synonymous_variant 0.2
rpoC 763573 c.204G>C synonymous_variant 0.22
rpoC 763594 c.225C>T synonymous_variant 0.14
rpoC 763666 c.297G>T synonymous_variant 0.14
rpoC 763732 c.363C>T synonymous_variant 0.17
rpoC 763744 c.375G>C synonymous_variant 0.12
rpoC 764278 c.909A>G synonymous_variant 0.14
rpoC 764284 c.915G>C synonymous_variant 0.15
rpoC 764296 c.927G>C synonymous_variant 0.21
rpoC 764320 c.951C>T synonymous_variant 0.27
rpoC 764344 c.975C>T synonymous_variant 0.22
rpoC 764353 c.984G>T synonymous_variant 0.28
rpoC 764365 c.996C>T synonymous_variant 0.16
rpoC 764377 c.1008C>G synonymous_variant 0.11
rpoC 764458 c.1089G>C synonymous_variant 0.12
rpoC 764461 c.1092A>G synonymous_variant 0.14
rpoC 764497 c.1128A>G synonymous_variant 0.14
rpoC 764527 c.1158C>T synonymous_variant 0.14
rpoC 764530 c.1161C>T synonymous_variant 0.14
rpoC 764545 c.1176C>G synonymous_variant 0.15
rpoC 764548 c.1179G>T synonymous_variant 0.15
rpoC 764605 c.1236G>C synonymous_variant 0.2
rpoC 764611 c.1242G>T synonymous_variant 0.23
rpoC 764662 c.1293G>C synonymous_variant 0.13
rpoC 764812 c.1443C>G synonymous_variant 0.16
rpoC 764815 c.1446A>G synonymous_variant 0.13
rpoC 764962 c.1593G>C synonymous_variant 0.16
rpoC 764968 c.1599T>C synonymous_variant 0.18
rpoC 765478 c.2109T>C synonymous_variant 0.21
rpoC 765524 p.Ala719Thr missense_variant 0.22
rpoC 765844 c.2475C>G synonymous_variant 0.13
rpoC 765979 c.2610C>G synonymous_variant 0.13
rpoC 766012 c.2643C>G synonymous_variant 0.15
rpoC 766549 c.3180G>C synonymous_variant 0.12
rpoC 766573 c.3204T>G synonymous_variant 0.14
rpoC 766837 c.3468G>C synonymous_variant 0.34
rpoC 766843 c.3474T>G synonymous_variant 0.33
rpoC 767002 c.3633G>C synonymous_variant 0.29
rpoC 767008 c.3639G>A synonymous_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781655 c.96T>C synonymous_variant 0.17
rpsL 781658 c.99A>G synonymous_variant 0.13
rpsL 781829 c.270G>C synonymous_variant 0.26
rpsL 781832 c.273T>G synonymous_variant 0.26
rpsL 781865 c.306G>C synonymous_variant 0.12
rplC 800672 c.-137G>C upstream_gene_variant 0.13
fbiC 1303512 c.582T>C synonymous_variant 0.17
fbiC 1303515 c.585G>C synonymous_variant 0.17
fbiC 1303525 p.Ser199Glu missense_variant 0.15
fbiC 1303896 c.966G>C synonymous_variant 0.21
fbiC 1303900 p.Val324Leu missense_variant 0.21
fbiC 1303920 c.990C>G synonymous_variant 0.27
fbiC 1304958 c.2028T>C synonymous_variant 0.15
fbiC 1304973 c.2043C>G synonymous_variant 0.16
Rv1258c 1406791 p.Ser184Pro missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471985 n.140T>C non_coding_transcript_exon_variant 0.2
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.17
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.29
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.29
rrl 1474135 n.478G>A non_coding_transcript_exon_variant 0.14
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.22
rrl 1474220 n.563G>A non_coding_transcript_exon_variant 0.22
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.23
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.15
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.16
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.12
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.31
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.32
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.34
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.32
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.3
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.28
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.34
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.34
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.22
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.21
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.16
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.16
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.24
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.18
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.13
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.14
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.13
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.17
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.17
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.25
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.33
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.21
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.21
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.34
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.32
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.15
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.31
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.13
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.16
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.26
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.26
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.13
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.17
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.24
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.24
rpsA 1833667 c.126C>G synonymous_variant 0.27
rpsA 1833781 c.240T>C synonymous_variant 0.13
rpsA 1833811 c.270G>C synonymous_variant 0.2
rpsA 1833829 c.288A>G synonymous_variant 0.13
rpsA 1833832 c.291G>A synonymous_variant 0.15
rpsA 1833838 c.297G>T synonymous_variant 0.16
rpsA 1833841 c.300C>G synonymous_variant 0.19
rpsA 1833847 c.306C>G synonymous_variant 0.18
rpsA 1833850 c.309C>G synonymous_variant 0.19
rpsA 1833856 c.315A>G synonymous_variant 0.22
rpsA 1833877 c.336C>T synonymous_variant 0.2
rpsA 1833894 p.Ala118Glu missense_variant 0.2
rpsA 1833928 c.387G>C synonymous_variant 0.16
rpsA 1834069 c.528G>C synonymous_variant 0.15
rpsA 1834114 c.573G>C synonymous_variant 0.29
rpsA 1834246 c.705G>C synonymous_variant 0.2
rpsA 1834249 c.708T>C synonymous_variant 0.2
rpsA 1834255 c.714C>G synonymous_variant 0.2
rpsA 1834294 c.753G>C synonymous_variant 0.16
rpsA 1834298 p.Gln253Glu missense_variant 0.16
rpsA 1834384 c.843A>G synonymous_variant 0.12
rpsA 1834411 c.870T>C synonymous_variant 0.12
rpsA 1834423 c.882G>T synonymous_variant 0.15
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.17
rpsA 1834465 c.924T>C synonymous_variant 0.2
rpsA 1834468 c.927A>G synonymous_variant 0.2
rpsA 1834474 c.933C>T synonymous_variant 0.18
rpsA 1834489 c.948T>C synonymous_variant 0.18
rpsA 1834528 c.987T>C synonymous_variant 0.2
rpsA 1834534 c.993C>G synonymous_variant 0.15
rpsA 1834574 p.Met345Leu missense_variant 0.14
rpsA 1834733 p.Ala398Pro missense_variant 0.22
rpsA 1834738 c.1197A>G synonymous_variant 0.25
rpsA 1834753 c.1212T>C synonymous_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.16
PPE35 2167865 c.2748G>C synonymous_variant 0.23
PPE35 2167868 c.2745A>C synonymous_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 1.0
fbiD 3339385 p.Asp90Asn missense_variant 1.0
rpoA 3878310 c.198G>C synonymous_variant 0.12
rpoA 3878313 c.195G>C synonymous_variant 0.12
rpoA 3878391 c.117T>C synonymous_variant 0.12
rpoA 3878406 c.102G>C synonymous_variant 0.23
clpC1 4038584 c.2121G>C synonymous_variant 0.17
clpC1 4038740 c.1965G>C synonymous_variant 0.16
clpC1 4038773 c.1932T>C synonymous_variant 0.12
clpC1 4038896 c.1809C>A synonymous_variant 0.26
clpC1 4038905 c.1800A>C synonymous_variant 0.24
clpC1 4038911 c.1794G>T synonymous_variant 0.13
clpC1 4039073 c.1632C>T synonymous_variant 0.13
clpC1 4039145 c.1560G>C synonymous_variant 0.12
clpC1 4039499 c.1206G>C synonymous_variant 0.14
clpC1 4039793 c.912C>G synonymous_variant 0.17
clpC1 4039814 c.891C>G synonymous_variant 0.12
clpC1 4039831 c.874T>C synonymous_variant 0.18
clpC1 4039832 c.873C>G synonymous_variant 0.18
clpC1 4039889 c.816G>C synonymous_variant 0.14
clpC1 4039898 c.807C>G synonymous_variant 0.13
clpC1 4040431 c.274T>C synonymous_variant 0.15
clpC1 4040435 c.270G>C synonymous_variant 0.15
clpC1 4040648 c.57G>A synonymous_variant 0.22
embC 4240803 p.Tyr314Phe missense_variant 0.14
aftB 4269258 c.-422C>G upstream_gene_variant 0.2
ubiA 4269270 p.Val188Ala missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0