TB-Profiler result

Run: ERR9285979
Summary

Run ID: ERR9285979

Sample name:

Date: 02-04-2023 11:48:21

Number of reads: 2979905

Percentage reads mapped: 81.33

Strain: lineage3.1.1

Drug-resistance: RR-TB

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
lineage3.1.1 East-African-Indian CAS1-Kili 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
rpoB 761099 p.Ser431Arg missense_variant 0.11 rifampicin
rpoB 761196 p.Leu464Met missense_variant 0.13 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.24 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.21 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.17 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
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
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761123 c.1317G>C synonymous_variant 0.16
rpoB 761132 c.1326G>C synonymous_variant 0.16
rpoB 761133 c.1327T>C synonymous_variant 0.16
rpoB 761138 c.1332C>G synonymous_variant 0.17
rpoB 761147 c.1341C>T synonymous_variant 0.15
rpoB 761150 c.1344A>T synonymous_variant 0.16
rpoB 761156 c.1350G>C synonymous_variant 0.16
rpoB 761165 c.1359G>C synonymous_variant 0.16
rpoB 761168 c.1362C>G synonymous_variant 0.16
rpoB 761171 c.1365C>T synonymous_variant 0.16
rpoB 761180 c.1374A>C synonymous_variant 0.16
rpoB 761186 p.Glu460Asp missense_variant 0.15
rpoB 761195 c.1389G>C synonymous_variant 0.12
rpoB 761204 c.1398C>T synonymous_variant 0.12
rpoB 761207 c.1401C>T synonymous_variant 0.12
rpoB 761213 c.1407G>C synonymous_variant 0.12
rpoB 761234 c.1428G>C synonymous_variant 0.11
rpoB 761249 c.1443A>G synonymous_variant 0.11
rpoB 762209 c.2403C>G synonymous_variant 0.12
rpoB 762212 c.2406G>C synonymous_variant 0.12
rpoB 762233 c.2427G>C synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762929 c.-441G>C upstream_gene_variant 0.1
rpoC 762959 c.-411G>C upstream_gene_variant 0.11
rpoC 762962 c.-408C>T upstream_gene_variant 0.11
rpoC 762971 c.-399G>C upstream_gene_variant 0.16
rpoC 762989 c.-381G>C upstream_gene_variant 0.16
rpoC 762995 c.-375G>C upstream_gene_variant 0.17
rpoB 763005 p.Cys1067Val missense_variant 0.17
rpoB 763014 p.Met1070Leu missense_variant 0.19
rpoB 763017 p.Gln1071Glu missense_variant 0.19
rpoC 763028 c.-342T>C upstream_gene_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763040 c.-330C>G upstream_gene_variant 0.24
rpoC 763053 c.-317_-315delTTGinsCTC upstream_gene_variant 0.22
rpoC 763070 c.-300T>C upstream_gene_variant 0.19
rpoB 763074 p.Thr1090Val missense_variant 0.19
rpoB 763077 p.Val1091Pro missense_variant 0.15
rpoC 763094 c.-276G>C upstream_gene_variant 0.16
rpoC 764485 c.1116G>C synonymous_variant 0.13
rpoC 764491 c.1122G>C synonymous_variant 0.13
rpoC 764497 c.1128A>G synonymous_variant 0.12
rpoC 764498 p.Ser377Ala missense_variant 0.12
rpoC 764551 c.1182G>T synonymous_variant 0.12
rpoC 764566 c.1197C>G synonymous_variant 0.15
rpoC 764575 c.1206T>G synonymous_variant 0.14
rpoC 764581 c.1212T>C synonymous_variant 0.14
rpoC 764582 p.Leu405Met missense_variant 0.14
rpoC 764605 c.1236G>C synonymous_variant 0.13
rpoC 764611 c.1242G>T synonymous_variant 0.14
rpoC 764620 c.1251G>C synonymous_variant 0.13
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764644 c.1275G>C synonymous_variant 0.19
rpoC 764650 c.1281G>T synonymous_variant 0.18
rpoC 764662 c.1293G>C synonymous_variant 0.18
rpoC 764706 p.Leu446Gln missense_variant 0.15
rpoC 764716 c.1347G>C synonymous_variant 0.18
rpoC 764746 c.1377G>T synonymous_variant 0.15
rpoC 764752 c.1383G>C synonymous_variant 0.12
rpoC 764759 p.Asn464Asp missense_variant 0.12
rpoC 764764 c.1395T>C synonymous_variant 0.12
rpoC 764780 p.Ser471Cys missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778451 c.-539C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.18
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.18
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.18
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.15
rrs 1472288 n.443A>T non_coding_transcript_exon_variant 0.16
rrs 1472289 n.444T>C non_coding_transcript_exon_variant 0.16
rrs 1472290 n.445C>T non_coding_transcript_exon_variant 0.16
rrs 1472293 n.448C>A non_coding_transcript_exon_variant 0.16
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 0.16
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.15
rrs 1472326 n.481T>A non_coding_transcript_exon_variant 0.16
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.16
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.16
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.16
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.17
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.18
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.2
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.19
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.22
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.21
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.23
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.2
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.17
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.17
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.14
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.12
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.13
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.12
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.12
rrs 1472685 n.840G>A non_coding_transcript_exon_variant 0.13
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.14
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.14
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.17
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.17
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.18
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.18
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.2
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.21
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.2
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.2
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.26
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.22
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.22
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.22
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.23
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.2
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.2
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.22
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.22
rrs 1473127 n.1282G>A non_coding_transcript_exon_variant 0.23
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.26
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.2
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.2
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.18
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.18
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.17
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.16
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.12
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.12
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.12
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.14
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.13
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.16
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.15
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.15
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.15
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.12
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.12
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.19
rrl 1474664 n.1007G>A non_coding_transcript_exon_variant 0.18
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.14
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.14
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.14
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.19
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.22
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.22
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.22
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.21
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.21
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.18
rrl 1474823 n.1166C>A non_coding_transcript_exon_variant 0.18
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.17
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.17
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.17
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.17
rrl 1474904 n.1247G>T non_coding_transcript_exon_variant 0.11
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.17
rrl 1475697 n.2040C>A non_coding_transcript_exon_variant 0.18
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.18
rrl 1475702 n.2045G>T non_coding_transcript_exon_variant 0.17
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.17
rrl 1475740 n.2083G>C non_coding_transcript_exon_variant 0.26
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.25
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.25
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.25
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.25
rrl 1475766 n.2109G>C non_coding_transcript_exon_variant 0.19
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.26
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.27
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.27
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.27
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.27
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.27
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.26
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.27
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.27
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.27
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.31
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.28
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.25
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.21
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.19
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.18
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.14
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.11
rrl 1476213 n.2556G>T non_coding_transcript_exon_variant 0.12
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.14
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.16
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.16
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.16
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.14
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 0.12
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.1
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.11
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.21
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.23
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.26
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.22
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.21
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.21
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.21
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.19
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.19
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.19
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.18
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.13
rpsA 1833979 c.438T>C synonymous_variant 0.13
rpsA 1833994 c.453G>C synonymous_variant 0.12
rpsA 1833997 c.456G>C synonymous_variant 0.12
rpsA 1834000 c.459G>C synonymous_variant 0.12
rpsA 1834009 c.468C>T synonymous_variant 0.12
rpsA 1834012 c.471G>T synonymous_variant 0.12
rpsA 1834024 c.483G>C synonymous_variant 0.12
rpsA 1834030 c.489C>G synonymous_variant 0.13
rpsA 1834034 p.Ile165Val missense_variant 0.12
rpsA 1834039 c.498C>A synonymous_variant 0.12
rpsA 1834069 c.528G>C synonymous_variant 0.12
rpsA 1834336 c.795C>G synonymous_variant 0.12
rpsA 1834348 c.807T>C synonymous_variant 0.12
rpsA 1834395 p.Arg285Gln missense_variant 0.12
rpsA 1834411 c.870T>C synonymous_variant 0.1
rpsA 1834417 c.876G>C synonymous_variant 0.11
rpsA 1834423 c.882G>C synonymous_variant 0.11
rpsA 1834427 p.Ile296Val missense_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 2170461 p.Gly51Glu missense_variant 1.0
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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039586 c.1119G>C synonymous_variant 0.11
clpC1 4039610 c.1095G>C synonymous_variant 0.13
clpC1 4039616 c.1089G>C synonymous_variant 0.13
clpC1 4040033 c.672G>C synonymous_variant 0.11
clpC1 4040063 c.642G>C synonymous_variant 0.11
clpC1 4040069 c.636G>C synonymous_variant 0.11
clpC1 4040087 c.618G>C synonymous_variant 0.11
clpC1 4040090 c.615T>C synonymous_variant 0.12
clpC1 4040093 c.612C>G synonymous_variant 0.11
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
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