TB-Profiler result

Run: ERR4816604
Summary

Run ID: ERR4816604

Sample name:

Date: 01-04-2023 14:31:29

Number of reads: 716110

Percentage reads mapped: 91.7

Strain: lineage4.1.2

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
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 0.22 rifampicin
rpoB 761196 p.Leu464Met missense_variant 0.11 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.22 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.22 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.2 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
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 6907 c.-395C>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7864 p.Asn188Ile missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9648 p.Val783Met missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761102 c.1296A>G synonymous_variant 0.18
rpoB 761132 c.1326G>T synonymous_variant 0.14
rpoB 761133 c.1327T>C synonymous_variant 0.25
rpoB 761147 c.1341C>T synonymous_variant 0.12
rpoB 761150 c.1344A>T synonymous_variant 0.19
rpoB 761156 c.1350G>C synonymous_variant 0.11
rpoB 761159 c.1353G>A synonymous_variant 0.12
rpoB 761165 c.1359G>C synonymous_variant 0.18
rpoB 761168 c.1362C>G synonymous_variant 0.11
rpoB 761180 c.1374A>C synonymous_variant 0.11
rpoB 761186 p.Glu460Asp missense_variant 0.11
rpoB 761192 c.1386C>A synonymous_variant 0.11
rpoB 761195 c.1389G>C synonymous_variant 0.11
rpoB 761201 c.1395G>A synonymous_variant 0.1
rpoB 761204 c.1398C>T synonymous_variant 0.11
rpoB 761207 c.1401C>A synonymous_variant 0.11
rpoB 761219 c.1413G>C synonymous_variant 0.11
rpoB 761231 c.1425C>T synonymous_variant 0.12
rpoB 761234 c.1428G>T synonymous_variant 0.12
rpoC 763636 c.267T>C synonymous_variant 0.1
rpoC 763660 c.291T>G synonymous_variant 0.13
rpoC 763675 c.306C>G synonymous_variant 0.12
rpoC 763896 p.Lys176Arg missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764485 c.1116G>C synonymous_variant 0.11
rpoC 764491 c.1122G>T synonymous_variant 0.14
rpoC 764497 c.1128A>G synonymous_variant 0.14
rpoC 764503 c.1134G>T synonymous_variant 0.16
rpoC 764509 c.1140G>C synonymous_variant 0.1
rpoC 764512 c.1143G>C synonymous_variant 0.14
rpoC 764521 c.1152T>C synonymous_variant 0.11
rpoC 764593 c.1224C>T synonymous_variant 0.1
rpoC 764602 c.1233C>T synonymous_variant 0.14
rpoC 764605 c.1236G>T synonymous_variant 0.13
rpoC 764611 c.1242G>T synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766936 p.Glu1189Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.42
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.5
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.27
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.55
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.45
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.21
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.23
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.29
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.84
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.27
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.18
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.64
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.28
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.8
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.6
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.5
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.57
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.5
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.57
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.5
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.33
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.5
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.67
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.57
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.3
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.6
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.55
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.3
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.36
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.22
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.89
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.88
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.4
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.53
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.4
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.46
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.23
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.5
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.5
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.53
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.61
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.26
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.21
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.19
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.62
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.71
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.4
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.6
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.67
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.62
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.15
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.59
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.81
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.74
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.55
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.76
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.59
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.59
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.81
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.15
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.21
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.87
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.9
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.9
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.9
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.23
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.3
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.9
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.88
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.88
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.25
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.59
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.86
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.88
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.88
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.6
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.89
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.25
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.28
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.86
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.79
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.33
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.24
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.54
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.54
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.16
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.4
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.34
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.39
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.11
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.46
rrl 1473384 n.-274A>G upstream_gene_variant 0.15
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.5
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.5
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 1474249 n.592G>T non_coding_transcript_exon_variant 0.67
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.5
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.67
rrl 1474355 n.698A>G non_coding_transcript_exon_variant 0.67
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.67
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.67
rrl 1474393 n.736A>G non_coding_transcript_exon_variant 0.67
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.67
rrl 1474448 n.791T>C non_coding_transcript_exon_variant 1.0
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 1.0
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.6
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.6
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.6
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.6
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.75
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.67
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.67
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.75
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.8
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.87
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.81
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.57
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.82
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.64
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.44
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.38
rpsA 1834261 c.720A>G synonymous_variant 0.12
rpsA 1834264 c.723G>C synonymous_variant 0.12
rpsA 1834294 c.753G>C synonymous_variant 0.13
rpsA 1834298 p.Gln253Glu missense_variant 0.13
rpsA 1834306 c.765T>C synonymous_variant 0.13
rpsA 1834307 p.Asp256Gln missense_variant 0.13
rpsA 1834312 c.771G>A synonymous_variant 0.14
rpsA 1834327 c.786G>T synonymous_variant 0.15
rpsA 1834348 c.807T>C synonymous_variant 0.11
rpsA 1834354 c.813G>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288929 p.Gly105Ser missense_variant 0.14
pncA 2289131 c.111A>G synonymous_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518766 p.Thr218Ala missense_variant 0.13
ribD 2987112 p.Gly92Ser missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448924 p.Gly141Ser missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
ddn 3986861 c.18G>C synonymous_variant 0.11
embC 4240648 c.786C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0