TB-Profiler result

Run: ERR4822104
Summary

Run ID: ERR4822104

Sample name:

Date: 01-04-2023 17:38:17

Number of reads: 290389

Percentage reads mapped: 35.75

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 0.33 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.76 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491607 c.825G>A synonymous_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575405 p.Arg20Cys missense_variant 0.13
rpoB 761030 c.1224G>C synonymous_variant 0.67
rpoB 761037 c.1231T>C synonymous_variant 0.67
rpoB 761051 c.1245G>C synonymous_variant 1.0
rpoB 761054 c.1248G>C synonymous_variant 1.0
rpoB 761057 c.1251G>C synonymous_variant 1.0
rpoB 761060 c.1254C>G synonymous_variant 1.0
rpoB 761084 c.1278C>A synonymous_variant 0.5
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.5
rpoB 761096 c.1290G>C synonymous_variant 0.5
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.5
rpoB 761102 c.1296A>G synonymous_variant 0.5
rpoB 762300 p.Lys832* stop_gained 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762887 c.-483G>C upstream_gene_variant 0.4
rpoC 762899 c.-471G>C upstream_gene_variant 0.5
rpoC 762926 c.-444C>G upstream_gene_variant 0.4
rpoC 762929 c.-441G>C upstream_gene_variant 0.33
rpoC 762947 c.-423C>G upstream_gene_variant 0.25
rpoC 762971 c.-399G>C upstream_gene_variant 0.33
rpoC 763028 c.-342T>C upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763038 p.Thr1078Ala missense_variant 0.5
rpoC 763043 c.-327G>C upstream_gene_variant 0.71
rpoC 763053 c.-317T>C upstream_gene_variant 0.71
rpoC 763067 c.-303C>G upstream_gene_variant 0.29
rpoC 763070 c.-300T>C upstream_gene_variant 0.71
rpoB 763077 p.Val1091Ser missense_variant 0.71
rpoC 763103 c.-267G>C upstream_gene_variant 0.71
rpoC 763109 c.-261C>T upstream_gene_variant 0.25
rpoC 763115 c.-255T>C upstream_gene_variant 0.71
rpoB 763119 p.Asn1105Asp missense_variant 0.71
rpoC 763127 c.-243G>C upstream_gene_variant 0.75
rpoC 763133 c.-237G>C upstream_gene_variant 0.67
rpoC 763402 c.33C>G synonymous_variant 0.4
rpoC 763411 c.42T>G synonymous_variant 0.4
rpoC 763414 c.45T>C synonymous_variant 0.4
rpoC 763441 c.72C>G synonymous_variant 0.4
rpoC 763444 c.75T>C synonymous_variant 0.4
rpoC 763456 c.87A>G synonymous_variant 0.4
rpoC 763468 c.99G>C synonymous_variant 1.0
rpoC 763511 p.Cys48Gly missense_variant 1.0
rpoC 763517 p.Lys50Gln missense_variant 1.0
rpoC 763528 c.159G>C synonymous_variant 0.75
rpoC 763531 c.162G>C synonymous_variant 0.75
rpoC 763534 c.165T>C synonymous_variant 0.75
rpoC 763546 c.177A>G synonymous_variant 0.6
rpoC 763550 p.Tyr61Ala missense_variant 0.6
rpoC 763555 c.186C>T synonymous_variant 0.6
rpoC 763570 c.201G>C synonymous_variant 0.6
rpoC 763578 p.Phe70Tyr missense_variant 0.6
rpoC 763699 c.330G>T synonymous_variant 0.6
rpoC 763708 c.339G>C synonymous_variant 0.4
rpoC 763714 c.345G>C synonymous_variant 0.33
rpoC 763717 c.348T>C synonymous_variant 0.33
rpoC 763718 p.Leu117Val missense_variant 0.33
rpoC 763723 c.354G>C synonymous_variant 0.33
rpoC 763724 p.Asp119Asn missense_variant 0.33
rpoC 763729 c.360G>C synonymous_variant 0.33
rpoC 763732 c.363C>G synonymous_variant 0.33
rpoC 763735 c.366G>C synonymous_variant 0.33
rpoC 763744 c.375G>C synonymous_variant 0.33
rpoC 763751 p.Ile128Val missense_variant 0.5
rpoC 763772 p.Val135Met missense_variant 0.4
rpoC 764485 c.1116G>C synonymous_variant 0.17
rpoC 764491 c.1122G>T synonymous_variant 0.2
rpoC 764497 c.1128A>G synonymous_variant 0.18
rpoC 764503 c.1134G>T synonymous_variant 0.27
rpoC 764512 c.1143G>C synonymous_variant 0.38
rpoC 764521 c.1152T>C synonymous_variant 0.42
rpoC 764530 c.1161C>T synonymous_variant 0.27
rpoC 764536 c.1167G>C synonymous_variant 0.43
rpoC 764543 p.Thr392Ala missense_variant 0.4
rpoC 764548 c.1179G>C synonymous_variant 0.38
rpoC 764551 c.1182G>C synonymous_variant 0.13
rpoC 764573 p.Leu402Ile missense_variant 0.5
rpoC 764578 c.1209C>G synonymous_variant 0.5
rpoC 764581 c.1212T>C synonymous_variant 0.5
rpoC 764582 p.Leu405Met missense_variant 0.5
rpoC 764593 c.1224C>T synonymous_variant 0.33
rpoC 764602 c.1233C>T synonymous_variant 0.45
rpoC 764605 c.1236G>T synonymous_variant 0.5
rpoC 764611 c.1242G>T synonymous_variant 0.45
rpoC 764632 c.1263T>C synonymous_variant 0.43
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779221 p.Gly78Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781751 c.192G>C synonymous_variant 0.25
rpsL 781760 c.201T>C synonymous_variant 0.29
rpsL 781766 c.207C>T synonymous_variant 0.29
rpsL 781796 p.Met79Ile missense_variant 0.29
rpsL 781802 c.243G>C synonymous_variant 0.29
rpsL 781811 c.252C>T synonymous_variant 0.29
rpsL 781814 c.255C>T synonymous_variant 0.29
rpsL 781817 c.258G>T synonymous_variant 0.29
rpsL 781832 c.273T>C synonymous_variant 0.29
rpsL 781835 c.276T>C synonymous_variant 0.29
rpsL 781841 c.282C>T synonymous_variant 0.33
fbiC 1303147 p.Ala73Thr missense_variant 0.5
fbiC 1303868 p.Asp313Gly missense_variant 0.25
Rv1258c 1406935 p.Gly136Ser missense_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.5
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.5
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.81
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.87
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.87
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.87
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.91
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.82
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.91
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.94
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.75
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.8
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.8
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.67
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.75
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.15
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.8
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.87
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.53
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.82
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.94
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.86
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.86
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.85
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.78
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.71
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.75
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.5
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.67
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.89
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.2
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.74
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.19
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.8
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.76
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.77
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.76
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.2
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.79
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.81
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.29
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.58
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472840 n.995A>G non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.89
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.74
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.76
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.97
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.97
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.97
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.97
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.95
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.89
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.94
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 1.0
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 1.0
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.73
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.27
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 1.0
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.7
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 0.86
rrs 1473122 n.1278A>T non_coding_transcript_exon_variant 0.93
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.92
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.13
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.84
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.79
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.16
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.15
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.78
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 1.0
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 1.0
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 1.0
rrs 1473291 n.1446G>C non_coding_transcript_exon_variant 1.0
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 1.0
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 1.0
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 1.0
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 1.0
rrl 1473384 n.-274A>G upstream_gene_variant 1.0
rrl 1474163 n.506C>T non_coding_transcript_exon_variant 0.5
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.67
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.89
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.8
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.82
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.75
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.82
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.19
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.13
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.87
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.18
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.43
rrl 1474272 n.615C>T non_coding_transcript_exon_variant 0.43
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.8
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 1.0
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 1.0
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 1.0
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 1.0
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 1.0
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 1.0
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.83
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.8
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 1.0
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 1.0
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 1.0
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 1.0
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.5
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.5
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.5
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.5
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.67
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.13
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.13
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.83
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.13
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.9
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.96
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.91
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.87
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.74
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.57
inhA 1673450 c.-752C>A upstream_gene_variant 0.25
rpsA 1833897 p.Leu119Pro missense_variant 0.5
rpsA 1834234 c.693G>C synonymous_variant 0.22
rpsA 1834240 c.699T>C synonymous_variant 0.22
rpsA 1834246 c.705G>T synonymous_variant 0.22
rpsA 1834249 c.708T>C synonymous_variant 0.22
rpsA 1834258 c.717G>A synonymous_variant 0.25
rpsA 1834261 c.720A>G synonymous_variant 0.5
rpsA 1834264 c.723G>C synonymous_variant 0.44
rpsA 1834294 c.753G>C synonymous_variant 0.71
rpsA 1834298 p.Gln253Glu missense_variant 0.67
rpsA 1834306 c.765T>C synonymous_variant 0.67
rpsA 1834307 p.Asp256Gln missense_variant 0.67
rpsA 1834312 c.771G>A synonymous_variant 0.5
rpsA 1834327 c.786G>T synonymous_variant 0.4
rpsA 1834345 c.804C>T synonymous_variant 0.27
rpsA 1834348 c.807T>C synonymous_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103206 c.-164T>C upstream_gene_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
Rv1979c 2222758 p.Val136Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288700 p.Glu181Trp missense_variant 0.29
pncA 2289047 c.195C>T synonymous_variant 1.0
kasA 2519008 c.894C>T synonymous_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726208 p.Ile6Val missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642126 p.Ile198Val missense_variant 0.67
fbiB 3642467 c.933T>C synonymous_variant 0.2
embC 4241456 p.Ala532Thr missense_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242946 c.3086delG frameshift_variant 0.2
embB 4246987 c.474C>T synonymous_variant 0.14
aftB 4267936 p.Val301Leu missense_variant 0.29
gid 4407588 c.615A>G synonymous_variant 1.0