TB-Profiler result

Run: ERR4817464
Summary

Run ID: ERR4817464

Sample name:

Date: 01-04-2023 15:00:22

Number of reads: 626718

Percentage reads mapped: 80.4

Strain: lineage3.1.1

Drug-resistance: Other

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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
lineage3.1.1 East-African-Indian CAS1-Kili 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.44 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8414 c.1113C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.19
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.22
ccsA 620271 c.381C>G synonymous_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761990 c.2184G>C synonymous_variant 0.15
rpoB 762000 c.2194_2195delTCinsAG synonymous_variant 0.15
rpoB 762003 p.Asn733Arg missense_variant 0.14
rpoB 762009 p.Leu735Val missense_variant 0.15
rpoB 762024 p.Val740Ile missense_variant 0.12
rpoB 762029 c.2223C>G synonymous_variant 0.12
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>A synonymous_variant 0.12
rpoB 762071 p.Asp755Glu missense_variant 0.18
rpoB 762080 c.2274G>C synonymous_variant 0.17
rpoB 762085 p.Ala760Glu missense_variant 0.18
rpoB 762089 c.2283G>A synonymous_variant 0.18
rpoB 762110 c.2304G>C synonymous_variant 0.12
rpoB 762114 p.Ile770Val missense_variant 0.13
rpoB 762122 p.Asp772Glu missense_variant 0.14
rpoB 762143 c.2337T>C synonymous_variant 0.12
rpoB 762149 c.2343G>C synonymous_variant 0.17
rpoB 762156 p.Val784Ile missense_variant 0.17
rpoB 762167 c.2361T>C synonymous_variant 0.18
rpoB 762176 c.2370T>C synonymous_variant 0.12
rpoB 762177 p.Arg791Thr missense_variant 0.19
rpoB 762181 p.Asp792Ala missense_variant 0.2
rpoB 762185 c.2379G>C synonymous_variant 0.15
rpoB 762194 c.2388G>C synonymous_variant 0.21
rpoB 762200 c.2394C>T synonymous_variant 0.19
rpoB 762212 c.2406G>C synonymous_variant 0.12
rpoB 762233 c.2427G>C synonymous_variant 0.1
rpoB 762236 c.2430G>C synonymous_variant 0.1
rpoB 762245 c.2439G>C synonymous_variant 0.1
rpoB 762254 c.2448T>C synonymous_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763660 c.291T>G synonymous_variant 0.11
rpoC 763699 c.330G>T synonymous_variant 0.1
rpoC 763751 p.Ile128Val missense_variant 0.11
rpoC 764380 c.1011G>T synonymous_variant 0.14
rpoC 764485 c.1116G>C synonymous_variant 0.1
rpoC 764602 c.1233C>T synonymous_variant 0.11
rpoC 764632 c.1263T>C synonymous_variant 0.1
rpoC 764653 c.1284G>C synonymous_variant 0.1
rpoC 764713 c.1344G>C synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303781 p.Phe284Ser missense_variant 0.1
fbiC 1304649 c.1719C>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472101 n.256G>T non_coding_transcript_exon_variant 0.11
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.11
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.61
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.19
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.69
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.73
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.62
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.81
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.67
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.83
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.69
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.71
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.57
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.71
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.62
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.3
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.6
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.6
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.6
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.6
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.54
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.54
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.4
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.11
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.44
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.59
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.12
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.45
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472583 n.738T>C non_coding_transcript_exon_variant 0.11
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.39
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.58
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.53
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.13
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.43
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.9
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.86
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.56
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.41
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.47
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.27
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.73
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.73
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.7
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.6
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.38
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.51
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.39
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.45
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.49
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.47
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.51
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.16
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.45
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.37
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.47
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.47
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.56
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.38
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.57
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.55
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.16
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.52
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.81
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.71
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.16
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.75
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.6
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.15
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.14
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.86
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.61
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.67
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.93
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.87
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.9
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.97
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.61
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.74
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.95
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.8
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.3
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.85
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.45
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.25
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.85
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.95
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.95
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.14
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.9
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.85
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.57
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.72
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.31
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.29
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.69
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.67
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.75
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.81
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.74
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.68
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.26
rrs 1473266 n.1421A>G non_coding_transcript_exon_variant 0.15
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.92
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.55
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.56
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.76
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.21
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.21
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.75
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.17
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 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 1.0
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.5
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.5
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.5
rrl 1474517 n.860C>G non_coding_transcript_exon_variant 0.4
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.5
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.67
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 1.0
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 1.0
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 1.0
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 1.0
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 1.0
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 1.0
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1475707 n.2050T>C non_coding_transcript_exon_variant 1.0
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.67
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.67
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.67
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 1.0
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 1.0
rrl 1475761 n.2104C>A non_coding_transcript_exon_variant 0.67
rrl 1475762 n.2105G>C non_coding_transcript_exon_variant 1.0
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 1.0
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 1.0
rrl 1475766 n.2109_2110insTGT non_coding_transcript_exon_variant 1.0
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 1.0
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.33
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.33
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.75
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.67
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.83
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.33
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.5
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.5
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.33
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.33
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.83
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.67
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.67
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.26
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.84
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.77
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.65
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.62
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.4
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.43
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.43
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.43
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.33
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.33
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.33
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.33
inhA 1673973 c.-229G>A upstream_gene_variant 0.14
rpsA 1834234 c.693G>C synonymous_variant 0.11
rpsA 1834240 c.699T>C synonymous_variant 0.1
rpsA 1834249 c.708T>C synonymous_variant 0.14
rpsA 1834261 c.720A>G synonymous_variant 0.18
rpsA 1834264 c.723G>C synonymous_variant 0.18
rpsA 1834294 c.753G>C synonymous_variant 0.18
rpsA 1834298 p.Gln253Glu missense_variant 0.17
rpsA 1834306 c.765T>C synonymous_variant 0.15
rpsA 1834307 p.Asp256Gln missense_variant 0.15
rpsA 1834312 c.771G>A synonymous_variant 0.15
rpsA 1834327 c.786G>T synonymous_variant 0.16
rpsA 1834345 c.804C>T synonymous_variant 0.11
rpsA 1834348 c.807T>C synonymous_variant 0.12
rpsA 1834354 c.813G>C synonymous_variant 0.11
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 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518319 p.Asp69Asn missense_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878182 p.Asp109Gly missense_variant 0.13
clpC1 4040679 p.Ala9Asp missense_variant 0.12
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241585 c.1725delC frameshift_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408345 c.-143C>T upstream_gene_variant 1.0