TB-Profiler result

Run: ERR4821007
Summary

Run ID: ERR4821007

Sample name:

Date: 01-04-2023 17:00:41

Number of reads: 738823

Percentage reads mapped: 84.1

Strain: lineage1.2.2.2

Drug-resistance: RR-TB

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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 0.99
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA 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
rpoB 761127 p.Ser441Ala missense_variant 0.11 rifampicin
rpoB 761196 p.Leu464Met missense_variant 0.17 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.19 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_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 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
mshA 575305 c.-43C>T upstream_gene_variant 0.12
rpoB 761132 c.1326G>C synonymous_variant 0.12
rpoB 761133 c.1327T>C synonymous_variant 0.12
rpoB 761150 c.1344A>C synonymous_variant 0.16
rpoB 761159 c.1353G>C synonymous_variant 0.14
rpoB 761165 c.1359G>C synonymous_variant 0.14
rpoB 761174 c.1368T>C synonymous_variant 0.11
rpoB 761180 c.1374A>C synonymous_variant 0.12
rpoB 761186 p.Glu460Asp missense_variant 0.18
rpoB 761189 c.1383T>C synonymous_variant 0.18
rpoB 761195 c.1389G>C synonymous_variant 0.17
rpoB 761201 c.1395G>A synonymous_variant 0.17
rpoB 761207 c.1401C>A synonymous_variant 0.17
rpoB 761213 c.1407G>C synonymous_variant 0.15
rpoB 761219 c.1413G>C synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763578 p.Phe70Tyr missense_variant 0.18
rpoC 763600 c.231C>G synonymous_variant 0.2
rpoC 763606 c.237C>A synonymous_variant 0.17
rpoC 763609 c.240C>G synonymous_variant 0.11
rpoC 763615 c.246G>C synonymous_variant 0.24
rpoC 763618 c.249C>T synonymous_variant 0.11
rpoC 763621 c.251_252insTTCC frameshift_variant 0.13
rpoC 763623 c.255_258delCAAG frameshift_variant 0.12
rpoC 763630 c.261G>C synonymous_variant 0.11
rpoC 763633 c.264T>C synonymous_variant 0.12
rpoC 763642 c.273G>C synonymous_variant 0.13
rpoC 763647 p.Gly93Ala missense_variant 0.11
rpoC 763654 c.285C>T synonymous_variant 0.11
rpoC 763655 p.Glu96Asn missense_variant 0.11
rpoC 763660 c.291T>G synonymous_variant 0.21
rpoC 763663 c.294C>T synonymous_variant 0.11
rpoC 763666 c.297G>C synonymous_variant 0.22
rpoC 763669 c.300C>G synonymous_variant 0.12
rpoC 763672 c.303C>G synonymous_variant 0.12
rpoC 763675 c.306C>G synonymous_variant 0.12
rpoC 763699 c.330G>T synonymous_variant 0.12
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764485 c.1116G>C synonymous_variant 0.11
rpoC 764491 c.1122G>T synonymous_variant 0.15
rpoC 764497 c.1128A>G synonymous_variant 0.18
rpoC 764503 c.1134G>T synonymous_variant 0.14
rpoC 764512 c.1143G>C synonymous_variant 0.14
rpoC 764521 c.1152T>C synonymous_variant 0.18
rpoC 764530 c.1161C>T synonymous_variant 0.18
rpoC 764536 c.1167G>C synonymous_variant 0.18
rpoC 764543 p.Thr392Ala missense_variant 0.17
rpoC 764548 c.1179G>C synonymous_variant 0.2
rpoC 764573 p.Leu402Ile missense_variant 0.3
rpoC 764578 c.1209C>G synonymous_variant 0.3
rpoC 764581 c.1212T>C synonymous_variant 0.3
rpoC 764582 p.Leu405Met missense_variant 0.3
rpoC 764593 c.1224C>T synonymous_variant 0.35
rpoC 764602 c.1233C>T synonymous_variant 0.35
rpoC 764605 c.1236G>T synonymous_variant 0.35
rpoC 764611 c.1242G>T synonymous_variant 0.33
rpoC 764626 c.1257C>T synonymous_variant 0.32
rpoC 764632 c.1263T>C synonymous_variant 0.29
rpoC 764647 c.1278C>T synonymous_variant 0.22
rpoC 764650 c.1281G>T synonymous_variant 0.22
rpoC 764653 c.1284G>C synonymous_variant 0.22
rpoC 764656 c.1287C>G synonymous_variant 0.21
rpoC 764662 c.1293G>C synonymous_variant 0.25
rpoC 764677 c.1308C>G synonymous_variant 0.22
rpoC 764678 p.Lys437Gln missense_variant 0.22
rpoC 764701 c.1332C>G synonymous_variant 0.18
rpoC 764706 p.Leu446Gln missense_variant 0.2
rpoC 764713 c.1344G>C synonymous_variant 0.15
rpoC 765383 p.Met672Leu missense_variant 0.13
rpoC 765404 p.Leu679Val missense_variant 0.12
rpoC 765409 c.2040T>C synonymous_variant 0.11
rpoC 765412 c.2043T>C synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778082 c.-908T>C upstream_gene_variant 0.12
mmpR5 778088 c.-902C>G upstream_gene_variant 0.12
mmpR5 778094 c.-896A>G upstream_gene_variant 0.12
mmpS5 778642 p.Trp88* stop_gained 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.23
fbiC 1304115 c.1185A>G synonymous_variant 0.2
Rv1258c 1407006 p.Leu112Arg missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.17
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.16
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.5
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.41
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.59
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.57
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.6
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.76
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.74
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.74
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.23
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.62
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.48
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.58
rrs 1472274 n.429A>G non_coding_transcript_exon_variant 0.3
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 0.17
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.17
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.17
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>C non_coding_transcript_exon_variant 0.25
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.35
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.13
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.13
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.48
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.61
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.11
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.61
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.11
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.47
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.56
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.53
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.52
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.41
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.19
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.5
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 0.18
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.38
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.23
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.13
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.4
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.3
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.32
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.4
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.61
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.69
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.59
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.1
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.65
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.7
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.59
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.63
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.67
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.62
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.62
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.67
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.6
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.62
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.65
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.64
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.64
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.58
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.64
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.63
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.63
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.6
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.64
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.61
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.74
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.74
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.74
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.74
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.68
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.65
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.63
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.6
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.6
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.57
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.59
rrl 1473384 n.-274A>G upstream_gene_variant 0.25
rrl 1473390 n.-268A>C upstream_gene_variant 0.17
rrl 1474163 n.506C>T non_coding_transcript_exon_variant 0.67
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.67
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.67
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.67
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.67
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.67
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.67
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.93
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.38
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.22
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.5
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.5
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.4
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.5
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.67
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.36
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 0.25
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.33
rrl 1475761 n.2104C>T non_coding_transcript_exon_variant 0.17
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.3
rrl 1475763 n.2107_2108delAA non_coding_transcript_exon_variant 0.3
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 0.25
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.46
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.6
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.6
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.45
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.52
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.41
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.1
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.11
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.43
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.46
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.19
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.25
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.25
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.2
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.23
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.17
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.75
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.73
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.74
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.69
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.48
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.36
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.33
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.27
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.17
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.33
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.33
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.25
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.25
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.22
rpsA 1834240 c.699T>C synonymous_variant 0.12
rpsA 1834249 c.708T>C synonymous_variant 0.16
rpsA 1834261 c.720A>G synonymous_variant 0.17
rpsA 1834264 c.723G>C synonymous_variant 0.17
rpsA 1834294 c.753G>C synonymous_variant 0.16
rpsA 1834298 p.Gln253Glu missense_variant 0.15
rpsA 1834306 c.765T>C synonymous_variant 0.16
rpsA 1834307 p.Asp256Gln missense_variant 0.16
rpsA 1834312 c.771G>A synonymous_variant 0.17
rpsA 1834327 c.786G>T synonymous_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.19
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170534 p.Ala27Thr missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289496 c.-255G>A upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449215 c.715dupG frameshift_variant 0.25
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
fbiA 3641533 p.Ala331Thr missense_variant 1.0
clpC1 4039037 c.1668T>C synonymous_variant 0.12
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 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248157 c.1644A>G synonymous_variant 1.0
embB 4249330 p.Met939Ile missense_variant 0.22
aftB 4268377 c.457_459dupTGG conservative_inframe_insertion 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_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