TB-Profiler result

Run: ERR4819012
Summary

Run ID: ERR4819012

Sample name:

Date: 01-04-2023 15:52:30

Number of reads: 480449

Percentage reads mapped: 67.3

Strain: lineage1.1.2

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 0.99
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 0.13 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.96 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
gyrB 5534 p.Val99Met missense_variant 0.17
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 8150 c.849C>T synonymous_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8622 p.Arg441Trp missense_variant 0.15
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 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800848 p.Thr14Ser missense_variant 0.22
fbiC 1303051 p.Val41Met missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.25
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.33
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.33
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.33
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.71
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.56
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.56
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.92
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.93
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.93
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.81
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.81
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.71
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.57
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.29
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.6
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.4
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.83
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.97
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.95
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.96
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.96
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.97
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.97
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.97
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.96
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.91
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.91
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.6
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.6
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.8
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.8
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.67
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.8
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.5
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.83
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.33
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.4
rrs 1473008 n.1164delT non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.75
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.8
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.8
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 1.0
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 1.0
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 1.0
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.83
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.6
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.6
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.33
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.33
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.33
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.5
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.5
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.21
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.15
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.62
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.65
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.65
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.65
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.14
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 1.0
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 1.0
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 1.0
rrl 1475757 n.2100_2101insG non_coding_transcript_exon_variant 1.0
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.5
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.67
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.67
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 1.0
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.5
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.5
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.5
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.22
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.78
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.88
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.88
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.75
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.75
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.8
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.8
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.8
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.8
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
fabG1 1673560 p.Lys41Leu missense_variant 0.14
rpsA 1834027 p.Gln162His missense_variant 0.22
rpsA 1834189 c.648G>C synonymous_variant 0.29
rpsA 1834195 c.654G>C synonymous_variant 0.38
rpsA 1834210 c.669C>T synonymous_variant 0.25
rpsA 1834213 c.672G>A synonymous_variant 0.38
rpsA 1834219 c.678C>G synonymous_variant 0.29
rpsA 1834222 c.681T>C synonymous_variant 0.33
rpsA 1834225 c.684C>G synonymous_variant 0.33
rpsA 1834231 c.690T>C synonymous_variant 0.33
rpsA 1834246 c.705G>T synonymous_variant 0.43
rpsA 1834249 c.708T>C synonymous_variant 0.43
rpsA 1834252 c.711C>T synonymous_variant 0.29
rpsA 1834261 c.720A>G synonymous_variant 0.33
rpsA 1834264 c.723G>C synonymous_variant 0.33
rpsA 1834285 c.744G>C synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167862 c.2751G>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169961 p.Gly218Ser missense_variant 0.29
PPE35 2170696 c.-84A>G upstream_gene_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223136 p.Ala10Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714956 p.Tyr126Cys missense_variant 0.29
eis 2715322 p.Thr4Ser missense_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859504 c.915G>A synonymous_variant 0.14
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3066256 c.-65C>T upstream_gene_variant 0.11
thyA 3074206 p.Glu89Val missense_variant 0.22
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
whiB7 3568675 p.Ser2Leu missense_variant 0.12
alr 3840302 c.1119G>A synonymous_variant 0.13
alr 3841602 c.-182C>A upstream_gene_variant 0.4
rpoA 3877929 c.579C>T synonymous_variant 0.15
rpoA 3878163 c.344delG frameshift_variant 0.29
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 4244167 p.Ala312Val missense_variant 1.0
embA 4244408 c.1176G>A synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246464 p.Val1078Met missense_variant 0.12
embB 4247022 p.Ala170Glu missense_variant 0.18
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
ubiA 4269690 p.Tyr48* stop_gained 0.11
ethA 4326432 p.Leu348Phe missense_variant 1.0
ethA 4326685 p.Met263Ile missense_variant 0.2
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