TB-Profiler result

Run: ERR4818977
Summary

Run ID: ERR4818977

Sample name:

Date: 01-04-2023 15:51:21

Number of reads: 756887

Percentage reads mapped: 82.35

Strain: lineage4.1.2.1

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rpoB 761127 p.Ser441Ala missense_variant 0.12 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.6 streptomycin
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 6932 p.Gln565Lys missense_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7905 p.Phe202Leu missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.11
fgd1 490970 p.Glu63Val missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.3
rpoB 759620 c.-187A>C upstream_gene_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761150 c.1344A>C synonymous_variant 0.12
rpoB 761156 c.1350G>C synonymous_variant 0.12
rpoB 761159 c.1353G>C synonymous_variant 0.12
rpoB 761165 c.1359G>C synonymous_variant 0.13
rpoB 761180 c.1374A>C synonymous_variant 0.11
rpoB 762236 c.2430G>C synonymous_variant 0.1
rpoB 762239 c.2433G>A synonymous_variant 0.11
rpoB 762245 c.2439G>C synonymous_variant 0.11
rpoC 763570 c.201G>C synonymous_variant 0.12
rpoC 763642 c.273G>C synonymous_variant 0.16
rpoC 763660 c.291T>C synonymous_variant 0.11
rpoC 763699 c.330G>T synonymous_variant 0.12
rpoC 763708 c.339G>C synonymous_variant 0.12
rpoC 764485 c.1116G>C synonymous_variant 0.25
rpoC 764491 c.1122G>T synonymous_variant 0.25
rpoC 764497 c.1128A>G synonymous_variant 0.25
rpoC 764503 c.1134G>T synonymous_variant 0.21
rpoC 764509 c.1140G>C synonymous_variant 0.27
rpoC 764512 c.1143G>C synonymous_variant 0.24
rpoC 764521 c.1152T>C synonymous_variant 0.31
rpoC 764524 c.1155C>T synonymous_variant 0.27
rpoC 764530 c.1161C>T synonymous_variant 0.29
rpoC 764536 c.1167G>C synonymous_variant 0.36
rpoC 764543 p.Thr392Ala missense_variant 0.27
rpoC 764548 c.1179G>T synonymous_variant 0.29
rpoC 764566 c.1197C>G synonymous_variant 0.24
rpoC 764573 p.Leu402Ile missense_variant 0.19
rpoC 764578 c.1209C>G synonymous_variant 0.18
rpoC 764581 c.1212T>C synonymous_variant 0.24
rpoC 764582 p.Leu405Met missense_variant 0.28
rpoC 764602 c.1233C>T synonymous_variant 0.3
rpoC 764605 c.1236G>T synonymous_variant 0.32
rpoC 764611 c.1242G>T synonymous_variant 0.3
rpoC 764632 c.1263T>C synonymous_variant 0.29
rpoC 764647 c.1278C>T synonymous_variant 0.29
rpoC 764650 c.1281G>T synonymous_variant 0.29
rpoC 764653 c.1284G>C synonymous_variant 0.29
rpoC 764656 c.1287C>T synonymous_variant 0.26
rpoC 764662 c.1293G>C synonymous_variant 0.26
rpoC 764677 c.1308C>G synonymous_variant 0.3
rpoC 764678 p.Lys437Gln missense_variant 0.3
rpoC 764706 p.Leu446Gln missense_variant 0.25
rpoC 764713 c.1344G>C synonymous_variant 0.22
rpoC 764731 c.1362G>C synonymous_variant 0.19
rpoC 764737 c.1368G>C synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777269 c.1212T>A synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407079 c.261delC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472068 n.223T>G non_coding_transcript_exon_variant 0.19
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.21
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.21
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.47
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.55
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.63
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.62
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.14
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.68
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.55
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.69
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.8
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.6
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.4
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.5
rrs 1472290 n.445C>T non_coding_transcript_exon_variant 0.5
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.4
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.29
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.29
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.29
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.29
rrs 1472462 n.617T>G non_coding_transcript_exon_variant 0.4
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.4
rrs 1472473 n.628G>T non_coding_transcript_exon_variant 0.4
rrs 1472474 n.629C>G non_coding_transcript_exon_variant 0.5
rrs 1472476 n.631A>G non_coding_transcript_exon_variant 0.5
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.5
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.5
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.5
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.5
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.6
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.18
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.68
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.71
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.73
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.76
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.22
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.77
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.78
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.71
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.18
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.89
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.97
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.78
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.76
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.24
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.17
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.89
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.75
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.65
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.26
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.65
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.18
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.79
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.91
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.24
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.49
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.28
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.62
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.28
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.6
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.55
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.43
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.48
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.37
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.79
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.58
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.17
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.75
rrs 1472840 n.995A>G non_coding_transcript_exon_variant 0.4
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.88
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.7
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.95
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.75
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.16
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.95
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.89
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.15
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.14
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.11
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.14
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.93
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.66
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.64
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.93
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.94
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.94
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.9
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.64
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.67
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.86
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.69
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.81
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.65
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.81
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.85
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.85
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.84
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.8
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.63
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.74
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.76
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.68
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.76
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.71
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.69
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.68
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.11
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.79
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.66
rrs 1473284 n.1439A>T non_coding_transcript_exon_variant 0.11
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.74
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.12
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.15
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.79
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.15
rrl 1473384 n.-274A>G upstream_gene_variant 0.24
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 1.0
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 1.0
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.67
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.67
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.67
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.75
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.75
rrl 1474634 n.977T>G non_coding_transcript_exon_variant 0.75
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.75
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.75
rrl 1474658 n.1001A>G non_coding_transcript_exon_variant 0.5
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.5
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.67
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.67
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.67
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.75
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.67
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.75
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.86
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 1.0
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.75
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.67
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.67
rrl 1475743 n.2086T>C non_coding_transcript_exon_variant 0.25
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.57
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 0.5
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.88
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.43
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 0.57
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 1.0
rrl 1475783 n.2126T>C non_coding_transcript_exon_variant 0.5
rrl 1475794 n.2137A>G non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.55
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.64
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.18
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.55
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.64
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.18
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.56
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.16
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.85
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.85
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.72
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.71
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.73
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.64
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.65
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.47
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.44
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.22
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.41
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.41
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.41
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.18
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.24
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.18
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.41
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.44
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.25
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.25
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.25
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.31
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.31
rrl 1476600 n.2943A>C non_coding_transcript_exon_variant 0.2
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.18
fabG1 1673500 p.Thr21Ser missense_variant 0.15
rpsA 1834249 c.708T>C synonymous_variant 0.12
rpsA 1834261 c.720A>G synonymous_variant 0.15
rpsA 1834264 c.723G>C synonymous_variant 0.15
rpsA 1834294 c.753G>C synonymous_variant 0.1
rpsA 1834298 p.Gln253Glu missense_variant 0.17
rpsA 1834303 c.762T>C synonymous_variant 0.14
rpsA 1834306 c.765T>C synonymous_variant 0.15
rpsA 1834307 p.Asp256Asn missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170385 c.228G>T synonymous_variant 0.18
PPE35 2170392 p.Gly74Ala missense_variant 0.18
PPE35 2170400 c.213G>C synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518798 c.684G>C synonymous_variant 0.11
kasA 2518879 c.765A>G synonymous_variant 0.11
kasA 2519045 p.His311Asn missense_variant 0.18
thyX 3067391 c.555G>A synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612661 c.456G>A synonymous_variant 0.18
Rv3236c 3612989 p.Leu43Ser missense_variant 0.11
clpC1 4039471 p.Ile412Val missense_variant 0.29
embC 4240648 c.786C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244184 p.Ser318Leu missense_variant 0.13
embA 4244295 c.1064delC frameshift_variant 0.2
embA 4244673 p.Glu481Lys missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0