TB-Profiler result

Run: ERR4816009
Summary

Run ID: ERR4816009

Sample name:

Date: 01-04-2023 14:11:20

Number of reads: 594769

Percentage reads mapped: 90.62

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.48 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.19 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.29 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.21 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
gyrB 6124 c.885C>T synonymous_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 8546 c.1245T>C synonymous_variant 0.12
gyrA 8555 c.1254G>C synonymous_variant 0.12
gyrA 8558 c.1257C>G synonymous_variant 0.12
gyrA 8561 c.1260A>G synonymous_variant 0.12
gyrA 8562 c.1261C>T synonymous_variant 0.11
gyrA 8573 c.1272G>C synonymous_variant 0.11
gyrA 8597 c.1296C>G synonymous_variant 0.1
gyrA 8603 c.1302A>C synonymous_variant 0.12
gyrA 8609 c.1308G>C synonymous_variant 0.11
gyrA 8619 c.1318T>C synonymous_variant 0.12
gyrA 8630 c.1329G>C synonymous_variant 0.12
gyrA 8633 c.1332C>G synonymous_variant 0.12
gyrA 8636 c.1335A>C synonymous_variant 0.12
gyrA 8642 c.1341A>G synonymous_variant 0.12
gyrA 8645 c.1344C>G synonymous_variant 0.12
gyrA 8655 p.Ile452Val missense_variant 0.13
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
rpoB 759615 c.-192A>C upstream_gene_variant 0.33
rpoB 759620 c.-187A>C upstream_gene_variant 0.29
rpoC 762911 c.-459C>T upstream_gene_variant 0.12
rpoC 762917 c.-453C>T upstream_gene_variant 0.12
rpoC 762920 c.-450C>T upstream_gene_variant 0.12
rpoC 762929 c.-441G>T upstream_gene_variant 0.12
rpoC 762944 c.-426C>T upstream_gene_variant 0.11
rpoC 762956 c.-414G>C upstream_gene_variant 0.12
rpoC 762962 c.-408C>T upstream_gene_variant 0.12
rpoC 762983 c.-387C>T upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763570 c.201G>C synonymous_variant 0.12
rpoC 763578 p.Phe70Tyr missense_variant 0.14
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
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
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471668 n.-178G>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.21
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.33
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.14
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.38
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.69
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.12
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.68
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.61
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.14
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.19
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.17
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.17
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.17
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.16
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.16
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.28
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.17
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.28
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.59
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.42
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.21
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.21
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.48
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.67
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.58
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.12
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.15
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.67
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.55
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.62
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.59
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.16
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.55
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.17
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.2
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.56
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.16
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.24
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.3
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.29
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.29
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.29
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.25
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.48
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.52
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.58
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.56
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.59
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.55
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.52
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.64
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.12
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.79
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.87
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.86
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.84
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.24
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.27
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.71
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.67
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.63
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.13
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.63
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.65
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.62
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.34
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.66
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.3
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.23
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.56
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.54
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.2
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.21
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.14
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.45
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.5
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.28
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.32
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.21
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.21
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.19
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.29
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.24
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.44
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.5
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.5
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.5
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.5
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.5
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.33
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.25
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.3
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.3
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.17
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.17
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.17
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.17
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.14
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.21
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.44
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.25
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.27
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.25
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.3
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 0.2
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.21
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.29
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.15
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.18
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.31
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.31
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.36
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.18
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.18
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.17
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.18
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.17
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.12
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.18
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.48
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.42
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.52
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.55
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.18
rpsA 1833622 c.81C>T synonymous_variant 0.11
rpsA 1833664 c.123C>G synonymous_variant 0.11
rpsA 1833667 c.126C>G 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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.21
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
kasA 2518144 c.30T>G synonymous_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074645 c.-174T>G upstream_gene_variant 0.25
thyA 3074648 c.-177T>G upstream_gene_variant 0.38
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>A synonymous_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 3474700 p.Gly232Ser missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3641357 p.Val272Ala missense_variant 1.0
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
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249673 p.Ser1054Pro missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4328209 c.-736C>A 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 4407873 c.330G>T synonymous_variant 1.0
gid 4407935 p.Leu90Val missense_variant 1.0
gid 4407944 p.Gln87Glu missense_variant 1.0