TB-Profiler result

Run: ERR4821276
Summary

Run ID: ERR4821276

Sample name:

Date: 01-04-2023 17:09:42

Number of reads: 3003745

Percentage reads mapped: 51.03

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 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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.67 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.43 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 7386 p.Ile29Leu missense_variant 0.12
gyrA 7394 c.93T>C synonymous_variant 0.12
gyrA 7406 c.105G>C synonymous_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7859 c.558A>G synonymous_variant 0.11
gyrA 7862 c.561C>G synonymous_variant 0.11
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 760263 p.Met153Leu missense_variant 0.12
rpoB 760266 p.Met154Leu missense_variant 0.12
rpoB 760273 p.Glu156Gly missense_variant 0.12
rpoB 760298 c.492G>C synonymous_variant 0.13
rpoB 760310 c.504G>C synonymous_variant 0.13
rpoB 760313 c.507G>C synonymous_variant 0.14
rpoB 760991 c.1185G>C synonymous_variant 0.14
rpoB 760997 c.1191G>C synonymous_variant 0.13
rpoB 761006 c.1200C>G synonymous_variant 0.12
rpoB 761013 p.Val403Ile missense_variant 0.12
rpoB 761027 c.1221A>G synonymous_variant 0.13
rpoB 761036 c.1230G>C synonymous_variant 0.14
rpoB 761037 c.1231T>C synonymous_variant 0.14
rpoB 761046 p.Ile414Val missense_variant 0.14
rpoB 761051 c.1245G>C synonymous_variant 0.15
rpoB 761054 c.1248G>C synonymous_variant 0.15
rpoB 761057 c.1251G>C synonymous_variant 0.17
rpoB 761150 c.1344A>C synonymous_variant 0.18
rpoB 761162 c.1356G>C synonymous_variant 0.15
rpoB 761165 c.1359G>C synonymous_variant 0.15
rpoB 761171 c.1365C>T synonymous_variant 0.15
rpoB 761175 c.1371_1372delGT frameshift_variant 0.16
rpoB 761180 c.1374_1375insGC frameshift_variant 0.15
rpoB 761189 c.1383T>C synonymous_variant 0.15
rpoB 761195 c.1389G>C synonymous_variant 0.15
rpoB 761196 p.Leu464Val missense_variant 0.16
rpoB 761207 c.1401C>T synonymous_variant 0.16
rpoB 761213 c.1407G>C synonymous_variant 0.14
rpoB 761537 c.1731C>G synonymous_variant 0.22
rpoB 761555 c.1749G>C synonymous_variant 0.25
rpoB 761558 c.1752C>G synonymous_variant 0.26
rpoB 761562 p.Ala586Ser missense_variant 0.27
rpoB 761565 p.Met587Leu missense_variant 0.26
rpoB 761570 c.1764T>C synonymous_variant 0.25
rpoB 761579 c.1773G>C synonymous_variant 0.28
rpoB 761600 c.1794T>C synonymous_variant 0.26
rpoB 761603 c.1797C>T synonymous_variant 0.26
rpoB 761612 c.1806G>T synonymous_variant 0.25
rpoB 761615 c.1809A>G synonymous_variant 0.24
rpoB 761627 c.1821C>T synonymous_variant 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762879 p.Met1025Leu missense_variant 0.2
rpoC 762896 c.-474G>C upstream_gene_variant 0.26
rpoC 762929 c.-441G>C upstream_gene_variant 0.27
rpoC 762932 c.-438G>C upstream_gene_variant 0.27
rpoC 762947 c.-423C>G upstream_gene_variant 0.27
rpoC 762962 c.-408C>T upstream_gene_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763052 c.-318G>C upstream_gene_variant 0.12
rpoC 763053 c.-317T>C upstream_gene_variant 0.13
rpoC 763058 c.-312C>G upstream_gene_variant 0.18
rpoC 763070 c.-300T>C upstream_gene_variant 0.21
rpoB 763075 p.Thr1090Ile missense_variant 0.22
rpoC 763094 c.-276G>C upstream_gene_variant 0.22
rpoC 763115 c.-255T>C upstream_gene_variant 0.24
rpoB 763126 p.Pro1107Gln missense_variant 0.23
rpoC 763148 c.-222G>C upstream_gene_variant 0.16
rpoC 763660 c.291T>C synonymous_variant 0.16
rpoC 763666 c.297G>C synonymous_variant 0.18
rpoC 763696 c.327T>C synonymous_variant 0.24
rpoC 763708 c.339G>C synonymous_variant 0.27
rpoC 763711 c.342G>C synonymous_variant 0.27
rpoC 763714 c.345G>A synonymous_variant 0.26
rpoC 763717 c.348T>C synonymous_variant 0.28
rpoC 763723 c.354G>C synonymous_variant 0.29
rpoC 763727 p.Leu120Met missense_variant 0.27
rpoC 763732 c.363C>G synonymous_variant 0.28
rpoC 763744 c.375G>C synonymous_variant 0.25
rpoC 763751 p.Ile128Val missense_variant 0.2
rpoC 763765 c.396T>C synonymous_variant 0.16
rpoC 764308 c.939G>C synonymous_variant 0.19
rpoC 764316 p.Ala316Val missense_variant 0.19
rpoC 764320 c.951C>G synonymous_variant 0.22
rpoC 764353 c.984G>C synonymous_variant 0.29
rpoC 764365 c.996C>T synonymous_variant 0.32
rpoC 764371 c.1002G>C synonymous_variant 0.32
rpoC 764380 c.1011G>C synonymous_variant 0.36
rpoC 764381 c.1012_1013delTCinsAG synonymous_variant 0.36
rpoC 764387 c.1018T>C synonymous_variant 0.34
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.31
rpoC 764428 c.1059G>C synonymous_variant 0.15
rpoC 764431 c.1062G>C synonymous_variant 0.15
rpoC 764432 p.Lys355Arg missense_variant 0.15
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.14
rpoC 764446 c.1077T>C synonymous_variant 0.15
rpoC 764449 c.1080G>C synonymous_variant 0.15
rpoC 764455 c.1086G>C synonymous_variant 0.18
rpoC 764458 c.1089G>C synonymous_variant 0.18
rpoC 764461 c.1092A>G synonymous_variant 0.2
rpoC 764470 c.1101C>G synonymous_variant 0.23
rpoC 764497 c.1128A>G synonymous_variant 0.23
rpoC 764498 p.Ser377Ala missense_variant 0.24
rpoC 764503 c.1134G>C synonymous_variant 0.31
rpoC 764509 c.1140G>C synonymous_variant 0.33
rpoC 764521 c.1152T>C synonymous_variant 0.39
rpoC 764533 c.1164C>T synonymous_variant 0.43
rpoC 764536 c.1167G>T synonymous_variant 0.44
rpoC 764548 c.1179G>T synonymous_variant 0.45
rpoC 764549 p.Pro394Thr missense_variant 0.42
rpoC 764561 p.Pro398Ala missense_variant 0.45
rpoC 764566 c.1197C>G synonymous_variant 0.45
rpoC 764575 c.1206T>G synonymous_variant 0.41
rpoC 764581 c.1212T>C synonymous_variant 0.43
rpoC 764582 p.Leu405Met missense_variant 0.42
rpoC 764611 c.1242G>C synonymous_variant 0.49
rpoC 764632 c.1263T>C synonymous_variant 0.4
rpoC 764635 c.1266C>G synonymous_variant 0.39
rpoC 764650 c.1281G>T synonymous_variant 0.41
rpoC 764660 p.Val431Ile missense_variant 0.36
rpoC 764677 c.1308C>G synonymous_variant 0.35
rpoC 764683 c.1314G>C synonymous_variant 0.3
rpoC 764692 c.1323C>T synonymous_variant 0.28
rpoC 764705 p.Leu446Ala missense_variant 0.17
rpoC 764911 c.1542A>G synonymous_variant 0.12
rpoC 764912 p.Met515Leu missense_variant 0.11
rpoC 764917 c.1548G>C synonymous_variant 0.14
rpoC 764923 c.1554A>G synonymous_variant 0.14
rpoC 764935 c.1566T>C synonymous_variant 0.16
rpoC 764948 c.1579_1581delTTGinsCTC synonymous_variant 0.17
rpoC 764953 c.1584G>C synonymous_variant 0.17
rpoC 764956 c.1587T>C synonymous_variant 0.18
rpoC 764958 p.Glu530Ala missense_variant 0.18
rpoC 764968 c.1599T>C synonymous_variant 0.2
rpoC 766075 c.2706C>G synonymous_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
rpsL 781760 c.201T>C synonymous_variant 0.13
rpsL 781794 p.Met79Leu missense_variant 0.15
rpsL 781802 c.243G>C synonymous_variant 0.16
rpsL 781805 c.246G>C synonymous_variant 0.16
rpsL 781808 c.249C>T synonymous_variant 0.15
rpsL 781811 c.252C>A synonymous_variant 0.16
rpsL 781817 c.258G>T synonymous_variant 0.15
rpsL 781829 c.270G>C synonymous_variant 0.12
rpsL 781832 c.273T>C synonymous_variant 0.13
rpsL 781838 c.279G>C synonymous_variant 0.12
rpsL 781841 c.282C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.4
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.38
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472256 n.411T>C non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 1.0
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 1.0
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 1.0
rrs 1472660 n.815T>A non_coding_transcript_exon_variant 1.0
rrs 1472666 n.821G>T non_coding_transcript_exon_variant 1.0
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.67
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.67
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 1.0
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.6
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.6
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.6
rrs 1472993 n.1148G>T non_coding_transcript_exon_variant 0.67
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.57
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.43
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.42
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.36
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.36
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.36
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.33
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.33
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.38
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.38
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.54
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.47
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.5
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.46
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.64
rrs 1473269 n.1424C>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.5
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.46
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.43
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.43
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.44
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.43
rrs 1473320 n.1475G>A non_coding_transcript_exon_variant 0.43
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.43
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 1.0
rrl 1474202 n.545T>A non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.75
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.67
rrl 1474488 n.831G>C non_coding_transcript_exon_variant 0.25
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.25
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.25
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.33
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.33
rrl 1474516 n.859C>G non_coding_transcript_exon_variant 0.4
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.43
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.5
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.8
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.8
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 1.0
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 1.0
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 1.0
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 1.0
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 1.0
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.67
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.67
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.67
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.67
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 1.0
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 1.0
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.78
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.6
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.6
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.6
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.64
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.64
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.56
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.38
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.3
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.27
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.4
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.38
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.38
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.33
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.62
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.75
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.75
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.75
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.75
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.67
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.33
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.71
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.6
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.6
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.4
rpsA 1833709 c.168C>G synonymous_variant 0.12
rpsA 1833721 c.180A>G synonymous_variant 0.11
rpsA 1833727 c.186G>C synonymous_variant 0.11
rpsA 1833734 p.Ala65Ser missense_variant 0.12
rpsA 1833769 c.228C>G synonymous_variant 0.12
rpsA 1833790 c.249T>C synonymous_variant 0.12
rpsA 1833856 c.315A>G synonymous_variant 0.12
rpsA 1833859 c.318C>G synonymous_variant 0.13
rpsA 1833874 c.333T>C synonymous_variant 0.16
rpsA 1833884 p.Thr115Asp missense_variant 0.13
rpsA 1833887 p.Ile116Val missense_variant 0.13
rpsA 1833893 p.Ala118Lys missense_variant 0.13
rpsA 1833896 p.Leu119Ile missense_variant 0.17
rpsA 1833907 p.Lys122Asn missense_variant 0.17
rpsA 1833912 p.Glu124Gly missense_variant 0.17
rpsA 1833915 p.Ala125Val missense_variant 0.17
rpsA 1833921 p.Lys127Thr missense_variant 0.16
rpsA 1833928 c.387G>C synonymous_variant 0.17
rpsA 1834384 c.843A>G synonymous_variant 0.15
rpsA 1834395 p.Arg285Gln missense_variant 0.2
rpsA 1834397 p.His286Val missense_variant 0.2
rpsA 1834411 c.870T>C synonymous_variant 0.33
rpsA 1834423 c.882G>T synonymous_variant 0.37
rpsA 1834427 p.Ile296Val missense_variant 0.38
rpsA 1834431 p.Val297Ala missense_variant 0.37
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.39
rpsA 1834456 c.915T>C synonymous_variant 0.42
rpsA 1834465 c.924T>C synonymous_variant 0.42
rpsA 1834468 c.927A>G synonymous_variant 0.42
rpsA 1834474 c.933C>G synonymous_variant 0.42
rpsA 1834482 p.Glu314Ala missense_variant 0.36
rpsA 1834486 p.Glu315Asp missense_variant 0.32
rpsA 1834489 c.948T>C synonymous_variant 0.33
rpsA 1834501 c.960G>C synonymous_variant 0.22
rpsA 1834513 c.972C>G synonymous_variant 0.13
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
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
folC 2746452 p.Gly383Ser missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
clpC1 4040024 c.681A>G synonymous_variant 0.12
clpC1 4040033 c.672G>C synonymous_variant 0.18
clpC1 4040063 c.642G>C synonymous_variant 0.27
clpC1 4040066 c.639G>C synonymous_variant 0.26
clpC1 4040069 c.636G>C synonymous_variant 0.27
clpC1 4040083 p.Thr208Ser missense_variant 0.3
clpC1 4040090 c.615T>G synonymous_variant 0.31
clpC1 4040096 p.Val203Ile missense_variant 0.28
clpC1 4040117 c.588A>G synonymous_variant 0.25
clpC1 4040126 c.579C>T synonymous_variant 0.2
clpC1 4040129 c.576C>G synonymous_variant 0.16
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