TB-Profiler result

Run: ERR4816476
Summary

Run ID: ERR4816476

Sample name:

Date: 01-04-2023 14:27:06

Number of reads: 1238666

Percentage reads mapped: 88.66

Strain: lineage3.1.2.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.12 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.34 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.33
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761051 c.1245G>C synonymous_variant 0.11
rpoB 761054 c.1248G>C synonymous_variant 0.1
rpoB 761084 c.1278C>A synonymous_variant 0.12
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.12
rpoB 761096 c.1290G>C synonymous_variant 0.1
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.11
rpoB 761102 c.1296A>G synonymous_variant 0.15
rpoB 762218 c.2412T>C synonymous_variant 0.12
rpoB 762357 p.Asp851Pro missense_variant 0.96
rpoB 762402 p.Tyr866His missense_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoB 763038 p.Thr1078Ala missense_variant 0.11
rpoC 763043 c.-327G>C upstream_gene_variant 0.12
rpoC 763053 c.-317T>C upstream_gene_variant 0.11
rpoC 763070 c.-300T>C upstream_gene_variant 0.14
rpoC 763622 p.Ala85Ser missense_variant 0.16
rpoC 763625 p.Lys86Arg missense_variant 0.11
rpoC 763630 c.261G>C synonymous_variant 0.14
rpoC 763633 c.264T>C synonymous_variant 0.14
rpoC 763642 c.273G>C synonymous_variant 0.18
rpoC 763648 c.279C>T synonymous_variant 0.21
rpoC 763657 p.Glu96Asp missense_variant 0.23
rpoC 763660 c.291T>C synonymous_variant 0.19
rpoC 763666 c.297G>C synonymous_variant 0.21
rpoC 763675 c.306C>G synonymous_variant 0.17
rpoC 763699 c.330G>T synonymous_variant 0.21
rpoC 763708 c.339G>C synonymous_variant 0.11
rpoC 763714 c.345G>C synonymous_variant 0.15
rpoC 763717 c.348T>C synonymous_variant 0.16
rpoC 763718 p.Leu117Val missense_variant 0.16
rpoC 763723 c.354G>C synonymous_variant 0.12
rpoC 763724 p.Asp119Asn missense_variant 0.12
rpoC 763729 c.360G>C synonymous_variant 0.13
rpoC 763732 c.363C>G synonymous_variant 0.13
rpoC 763735 c.366G>C synonymous_variant 0.12
rpoC 763744 c.375G>C synonymous_variant 0.11
rpoC 763751 p.Ile128Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777332 c.1149G>A 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 1472068 n.223T>G non_coding_transcript_exon_variant 0.5
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.43
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.43
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.25
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.3
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.48
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.35
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.29
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.43
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.44
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.45
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.87
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.39
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.42
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.39
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.45
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.15
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.67
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.5
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.5
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.5
rrs 1472427 n.582T>G non_coding_transcript_exon_variant 0.5
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.67
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.67
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.57
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.54
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.58
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.5
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.5
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.33
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.13
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.57
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.57
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.75
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.91
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.21
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.11
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.46
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.41
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.59
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.41
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.56
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.73
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.77
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.57
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.32
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.53
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.31
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.68
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.34
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.34
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.59
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.41
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.43
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.83
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.2
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.75
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.2
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.95
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.95
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.94
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.91
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.23
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.23
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.93
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.71
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.72
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.98
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.96
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.96
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.96
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.62
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.69
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.88
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.79
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.83
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.72
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.82
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.81
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.81
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.8
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.71
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.66
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.81
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.77
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.71
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.78
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.78
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.8
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.81
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.8
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.78
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.75
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.72
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.73
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.74
rrl 1473384 n.-274A>G upstream_gene_variant 0.45
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.67
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 0.8
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.67
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.67
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.67
rrl 1474634 n.977T>G non_coding_transcript_exon_variant 0.67
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.67
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.67
rrl 1474658 n.1001A>G non_coding_transcript_exon_variant 1.0
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 1.0
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 1474736 n.1084dupG non_coding_transcript_exon_variant 0.67
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.4
rrl 1474783 n.1126G>T non_coding_transcript_exon_variant 0.4
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.4
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.4
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.6
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.5
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 1.0
rrl 1474832 n.1175A>G non_coding_transcript_exon_variant 0.67
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.4
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 1.0
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.38
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.38
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.29
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.29
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.25
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.97
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.87
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.9
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.53
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.4
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.25
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.25
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.25
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.25
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.25
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.22
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.22
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.22
rpsA 1834246 c.705G>T synonymous_variant 0.12
rpsA 1834249 c.708T>C synonymous_variant 0.13
rpsA 1834261 c.720A>G synonymous_variant 0.17
rpsA 1834264 c.723G>C synonymous_variant 0.2
rpsA 1834294 c.753G>C synonymous_variant 0.31
rpsA 1834298 p.Gln253Glu missense_variant 0.3
rpsA 1834306 c.765T>C synonymous_variant 0.3
rpsA 1834307 p.Asp256Gln missense_variant 0.29
rpsA 1834312 c.771G>A synonymous_variant 0.29
rpsA 1834327 c.786G>T synonymous_variant 0.26
rpsA 1834345 c.804C>T synonymous_variant 0.19
rpsA 1834348 c.807T>C synonymous_variant 0.19
rpsA 1834354 c.813G>C synonymous_variant 0.17
rpsA 1834357 c.816T>C synonymous_variant 0.17
rpsA 1834360 c.819G>C synonymous_variant 0.17
rpsA 1834361 c.820T>C synonymous_variant 0.16
rpsA 1834366 c.825A>G synonymous_variant 0.16
rpsA 1834375 c.834G>C synonymous_variant 0.19
rpsA 1834378 c.837T>C synonymous_variant 0.19
rpsA 1834387 c.846C>T synonymous_variant 0.18
rpsA 1834411 c.870T>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102819 p.Val75Ala missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.4
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
eis 2714569 p.Ala255Gly missense_variant 0.3
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339394 p.Asn93His missense_variant 0.11
Rv3083 3448747 p.Arg82Trp missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475301 p.Ala432Asp missense_variant 0.13
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