TB-Profiler result

Run: ERR4816093
Summary

Run ID: ERR4816093

Sample name:

Date: 01-04-2023 14:14:09

Number of reads: 1591038

Percentage reads mapped: 72.94

Strain: lineage1.1.3

Drug-resistance: Other

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.58 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.15 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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576675 p.Arg443His missense_variant 1.0
rpoB 759886 p.Pro27His missense_variant 1.0
rpoB 761605 p.Leu600Pro missense_variant 0.11
rpoB 762026 c.2220G>C synonymous_variant 0.16
rpoB 762051 p.His749Tyr missense_variant 0.12
rpoB 762057 p.Ile751Val missense_variant 0.11
rpoB 762062 c.2256T>C synonymous_variant 0.12
rpoB 762065 c.2259T>C synonymous_variant 0.12
rpoB 762071 p.Asp755Glu missense_variant 0.12
rpoB 762080 c.2274G>C synonymous_variant 0.14
rpoB 762085 p.Ala760Glu missense_variant 0.13
rpoB 762089 c.2283G>A synonymous_variant 0.15
rpoB 762104 c.2298C>T synonymous_variant 0.16
rpoB 762110 c.2304G>C synonymous_variant 0.17
rpoB 762114 p.Ile770Val missense_variant 0.12
rpoB 762143 c.2337T>C synonymous_variant 0.13
rpoB 762149 c.2343G>C synonymous_variant 0.14
rpoB 762156 p.Val784Ile missense_variant 0.17
rpoB 762167 c.2361T>C synonymous_variant 0.17
rpoB 762176 c.2370T>C synonymous_variant 0.17
rpoB 762177 p.Arg791Thr missense_variant 0.18
rpoB 762181 p.Asp792Ala missense_variant 0.17
rpoB 762185 c.2379G>C synonymous_variant 0.18
rpoB 762194 c.2388G>C synonymous_variant 0.28
rpoB 762200 c.2394C>T synonymous_variant 0.42
rpoB 762233 c.2427G>C synonymous_variant 0.28
rpoB 762234 p.Pro810Ser missense_variant 0.26
rpoB 762245 c.2439G>C synonymous_variant 0.28
rpoB 762254 c.2448T>C synonymous_variant 0.29
rpoB 762266 c.2460T>C synonymous_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763699 c.330G>T synonymous_variant 0.14
rpoC 763708 c.339G>C synonymous_variant 0.11
rpoC 763714 c.345G>C synonymous_variant 0.14
rpoC 763717 c.348T>C synonymous_variant 0.14
rpoC 763718 p.Leu117Val missense_variant 0.14
rpoC 763751 p.Ile128Val missense_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 767308 c.3939C>T synonymous_variant 1.0
mmpL5 775619 c.2862G>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778099 p.Asp128Asn missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781796 p.Met79Ile missense_variant 0.1
rplC 801375 c.567C>T synonymous_variant 1.0
Rv1258c 1407190 c.123_150delTGGGCAGGCCTCGATCGTGGCCAGTGCG frameshift_variant 1.0
embR 1416574 c.774A>G synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471886 n.41G>T non_coding_transcript_exon_variant 0.14
rrs 1472068 n.223T>G non_coding_transcript_exon_variant 0.5
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.67
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.67
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.75
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.74
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.74
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.74
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.88
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.59
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.67
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.32
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.11
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.6
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.14
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.25
rrs 1472476 n.631A>G non_coding_transcript_exon_variant 1.0
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 1.0
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.69
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.12
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.75
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.75
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.79
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.78
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.77
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.88
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.78
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.81
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.4
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.97
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.88
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.88
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.69
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 1.0
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 1.0
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 0.83
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.11
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.62
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.27
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.55
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.4
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.59
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.63
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.56
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.61
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.56
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.54
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.81
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.25
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.5
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 0.95
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.23
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.71
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.24
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.95
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.98
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.78
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.55
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.22
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.21
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.91
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.6
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.59
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.92
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.89
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.91
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.9
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.51
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.49
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.89
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.85
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.84
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.36
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.42
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.83
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.83
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.83
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.42
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.79
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.43
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.42
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.88
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.9
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.64
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.65
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.76
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.88
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.87
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.14
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.94
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.83
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 1.0
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.17
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.92
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 1474205 n.548T>C non_coding_transcript_exon_variant 0.33
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 1.0
rrl 1475692 n.2035G>T non_coding_transcript_exon_variant 1.0
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.67
rrl 1475715 n.2058G>A non_coding_transcript_exon_variant 1.0
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 1.0
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.67
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.4
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.67
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.67
rrl 1475762 n.2105G>C non_coding_transcript_exon_variant 0.67
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.67
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.67
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 0.67
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.67
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.25
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.7
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.75
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.17
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.36
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.4
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.4
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.6
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.71
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.71
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.71
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.71
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.5
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.4
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.4
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.33
rrl 1475995 n.2338G>C non_coding_transcript_exon_variant 0.4
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.4
rrl 1475998 n.2341C>G non_coding_transcript_exon_variant 0.4
rrl 1476000 n.2343G>A non_coding_transcript_exon_variant 0.4
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.4
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.29
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.25
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.25
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.44
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.44
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.44
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.5
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.55
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.9
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.94
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.97
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.85
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.96
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.9
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.9
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.86
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.5
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.5
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.5
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.5
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.5
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.5
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.5
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.67
rpsA 1834195 c.654G>C synonymous_variant 0.27
rpsA 1834228 c.687C>T synonymous_variant 0.3
rpsA 1834234 c.693G>C synonymous_variant 0.29
rpsA 1834240 c.699T>C synonymous_variant 0.28
rpsA 1834246 c.705G>T synonymous_variant 0.27
rpsA 1834249 c.708T>C synonymous_variant 0.36
rpsA 1834261 c.720A>G synonymous_variant 0.44
rpsA 1834264 c.723G>C synonymous_variant 0.39
rpsA 1834294 c.753G>C synonymous_variant 0.3
rpsA 1834298 p.Gln253Glu missense_variant 0.28
rpsA 1834306 c.765T>C synonymous_variant 0.3
rpsA 1834307 p.Asp256Gln missense_variant 0.24
rpsA 1834312 c.771G>A synonymous_variant 0.24
rpsA 1834327 c.786G>T synonymous_variant 0.21
rpsA 1834348 c.807T>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167970 c.2643C>A synonymous_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747022 p.Val193Ile missense_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086767 c.-53A>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4038841 p.Val622Leu missense_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243056 p.Pro1065Leu missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245314 c.2082G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408252 c.-50A>G upstream_gene_variant 1.0
gid 4408338 c.-136A>G upstream_gene_variant 1.0
Rv1258c 1407190 c.122_150delNNNNNNNNNNNNNNNNNNNNNNNNNNNNA frameshift_variant 1.0