TB-Profiler result

Run: ERR2515055
Summary

Run ID: ERR2515055

Sample name:

Date: 17-08-2022 18:34:01

Number of reads: 680799

Percentage reads mapped: 83.3

Strain: lineage3

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 0.99
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 0.22 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 6610 c.-692C>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9390 p.Thr697Ala missense_variant 1.0
gyrA 9556 p.Thr752Lys missense_variant 0.11
fgd1 490751 c.-32T>G upstream_gene_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762080 c.2274G>C synonymous_variant 0.1
rpoB 762085 p.Ala760Glu missense_variant 0.1
rpoB 762110 c.2304G>C synonymous_variant 0.11
rpoB 762114 p.Ile770Val missense_variant 0.12
rpoB 762122 p.Asp772Glu missense_variant 0.11
rpoB 762125 c.2319G>A synonymous_variant 0.11
rpoB 762126 p.Val774Ser missense_variant 0.11
rpoB 762149 c.2343G>C synonymous_variant 0.11
rpoB 762156 p.Val784Ile missense_variant 0.12
rpoB 762167 c.2361T>C synonymous_variant 0.11
rpoB 762177 p.Arg791Ser missense_variant 0.12
rpoB 762200 c.2394C>T synonymous_variant 0.15
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762612 p.Ser936Arg missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763732 c.363C>G synonymous_variant 0.1
rpoC 763735 c.366G>C synonymous_variant 0.1
rpoC 764517 p.Asp383Gly missense_variant 0.15
rpoC 764611 c.1242G>T synonymous_variant 0.18
rpoC 764626 c.1257C>T synonymous_variant 0.12
rpoC 764650 c.1281G>T synonymous_variant 0.12
rpoC 764662 c.1293G>C synonymous_variant 0.12
rpoC 764706 p.Leu446Gln missense_variant 0.2
rpoC 764713 c.1344G>T synonymous_variant 0.13
rpoC 764731 c.1362G>C synonymous_variant 0.12
rpoC 766582 c.3213C>A synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303151 p.Gly74Ala missense_variant 0.13
embR 1416196 c.1152G>A synonymous_variant 0.18
embR 1416225 p.Glu375Gln missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471981 n.136C>T non_coding_transcript_exon_variant 0.15
rrs 1471996 n.151C>T non_coding_transcript_exon_variant 0.17
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.18
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.17
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.67
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.24
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.14
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.76
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.73
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.64
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.89
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.78
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.28
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.67
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.52
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.5
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.9
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.18
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.45
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.64
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.31
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.4
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.4
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.4
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.27
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.46
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.46
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.15
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.15
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.3
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.86
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.86
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.54
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.36
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.8
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.83
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.4
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.5
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.4
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.35
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.59
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.28
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.19
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.19
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.3
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.59
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.29
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.43
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.6
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.82
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.2
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.54
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.11
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.86
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.77
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.17
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.9
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.82
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.18
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.18
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.97
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.62
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.6
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.94
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.83
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.83
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.94
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.29
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.75
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.83
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.13
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.89
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.31
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.8
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.31
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.55
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.81
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.86
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.84
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.32
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.88
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.78
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.23
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.37
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.87
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.21
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.83
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.82
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.72
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.85
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.84
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.93
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.1
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.88
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.79
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.76
rrs 1473293 n.1449A>G non_coding_transcript_exon_variant 0.62
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.8
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.83
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.78
rrl 1473384 n.-274A>G upstream_gene_variant 0.4
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.82
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.3
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.3
rrl 1475731 n.2074G>A non_coding_transcript_exon_variant 0.2
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.2
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.86
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.8
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.18
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.22
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.7
rrl 1475760 n.2103C>A non_coding_transcript_exon_variant 0.33
rrl 1475762 n.2105G>C non_coding_transcript_exon_variant 0.75
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.18
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.18
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.75
rrl 1475783 n.2126T>C non_coding_transcript_exon_variant 0.14
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.11
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.64
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.5
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.27
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.64
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.82
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.82
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.18
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.4
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.5
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.2
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.33
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.27
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.27
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.55
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.45
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.45
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.27
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.91
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.36
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.13
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.29
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.86
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.67
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.62
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.25
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.11
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.81
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.32
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.72
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.71
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.64
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.6
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.64
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.6
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.6
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.6
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.6
rpsA 1833721 c.180A>G synonymous_variant 0.11
rpsA 1833727 c.186G>T synonymous_variant 0.11
rpsA 1833732 p.Pro64Leu missense_variant 0.12
rpsA 1833736 c.195C>T synonymous_variant 0.12
rpsA 1833742 c.201A>G synonymous_variant 0.12
rpsA 1833757 c.216C>T synonymous_variant 0.11
rpsA 1833949 c.408T>C synonymous_variant 0.11
rpsA 1833955 c.414G>C synonymous_variant 0.19
rpsA 1833970 c.429G>T synonymous_variant 0.23
rpsA 1833976 c.435C>G synonymous_variant 0.14
rpsA 1833979 c.438T>C synonymous_variant 0.33
rpsA 1833991 c.450C>A synonymous_variant 0.13
rpsA 1833994 c.453G>C synonymous_variant 0.31
rpsA 1833997 c.456G>C synonymous_variant 0.13
rpsA 1834000 c.459G>T synonymous_variant 0.21
rpsA 1834012 c.471G>C synonymous_variant 0.27
rpsA 1834015 c.474G>C synonymous_variant 0.12
rpsA 1834023 c.482_483insC frameshift_variant 0.13
rpsA 1834026 c.486delG frameshift_variant 0.12
rpsA 1834030 c.489C>T synonymous_variant 0.12
rpsA 1834034 p.Ile165Val missense_variant 0.12
rpsA 1834039 c.498C>T synonymous_variant 0.12
rpsA 1834040 p.Lys167Arg missense_variant 0.25
rpsA 1834043 p.Glu168Gln missense_variant 0.12
rpsA 1834046 p.Ile169Leu missense_variant 0.12
rpsA 1834051 c.510G>A synonymous_variant 0.12
rpsA 1834054 c.513C>T synonymous_variant 0.11
rpsA 1834294 c.753G>C synonymous_variant 0.1
rpsA 1834327 c.786G>T synonymous_variant 0.11
rpsA 1834345 c.804C>T synonymous_variant 0.15
rpsA 1834348 c.807T>C synonymous_variant 0.14
rpsA 1834354 c.813G>C synonymous_variant 0.13
rpsA 1834357 c.816T>C synonymous_variant 0.13
rpsA 1834360 c.819G>C synonymous_variant 0.13
rpsA 1834366 c.825A>G synonymous_variant 0.13
rpsA 1834375 c.834G>C synonymous_variant 0.13
rpsA 1834378 c.837T>C synonymous_variant 0.12
rpsA 1834387 c.846C>T synonymous_variant 0.12
rpsA 1834456 c.915T>C synonymous_variant 0.14
rpsA 1834459 c.918G>C synonymous_variant 0.15
rpsA 1834468 c.927A>G synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2715130 p.Arg68Leu missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.27
folC 2747372 p.Thr76Asn missense_variant 0.12
thyX 3067244 c.702C>A synonymous_variant 0.13
thyA 3074036 p.Cys146Ser missense_variant 0.12
thyA 3074402 p.Thr24Ala missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiB 3641658 p.Asp42His missense_variant 0.12
fbiB 3641665 p.Asp44Ala missense_variant 0.11
fbiB 3641668 p.Val45Ala missense_variant 0.11
fbiB 3642627 p.Arg365Cys missense_variant 0.12
alr 3841473 c.-53G>A upstream_gene_variant 1.0
alr 3841503 c.-83G>A upstream_gene_variant 0.12
embC 4241118 c.1257_1258insGGCAGC conservative_inframe_insertion 0.14
embC 4242073 c.2211C>T synonymous_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethR 4328102 c.555_560delGTCATT disruptive_inframe_deletion 0.12
ethR 4328111 p.Ala188Gly missense_variant 0.12
ethR 4328113 c.565_566insAATGAC stop_gained&disruptive_inframe_insertion 0.12
gid 4407588 c.615A>G synonymous_variant 1.0