TB-Profiler result

Run: ERR4829039
Summary

Run ID: ERR4829039

Sample name:

Date: 01-04-2023 19:14:44

Number of reads: 2391947

Percentage reads mapped: 81.39

Strain: lineage4.3.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.1 Euro-American (LAM) LAM9 None 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 0.25 rifampicin
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 0.98
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.21
mshA 576482 p.Val379Leu missense_variant 0.13
rpoB 761030 c.1224G>C synonymous_variant 0.12
rpoB 761037 c.1231T>C synonymous_variant 0.18
rpoB 761051 c.1245G>C synonymous_variant 0.22
rpoB 761054 c.1248G>C synonymous_variant 0.23
rpoB 761057 c.1251G>C synonymous_variant 0.22
rpoB 761060 c.1254C>G synonymous_variant 0.22
rpoB 761084 c.1278C>A synonymous_variant 0.22
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.22
rpoB 761096 c.1290G>C synonymous_variant 0.22
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.22
rpoB 761102 c.1296A>G synonymous_variant 0.26
rpoB 761123 c.1317G>C synonymous_variant 0.25
rpoB 761126 c.1320G>C synonymous_variant 0.25
rpoB 761132 c.1326G>C synonymous_variant 0.25
rpoB 761133 c.1327T>C synonymous_variant 0.26
rpoB 761150 c.1344A>T synonymous_variant 0.24
rpoB 761159 c.1353G>C synonymous_variant 0.24
rpoB 761165 c.1359G>C synonymous_variant 0.23
rpoB 761180 c.1374A>G synonymous_variant 0.12
rpoB 762143 c.2337T>C synonymous_variant 0.11
rpoB 762149 c.2343G>C synonymous_variant 0.12
rpoB 762156 p.Val784Ile missense_variant 0.11
rpoB 762167 c.2361T>C synonymous_variant 0.12
rpoB 762185 c.2379G>C synonymous_variant 0.11
rpoC 763053 c.-317T>C upstream_gene_variant 0.12
rpoC 763648 c.279C>T synonymous_variant 0.11
rpoC 763657 p.Glu96Asp missense_variant 0.11
rpoC 763660 c.291T>G synonymous_variant 0.11
rpoC 763666 c.297G>C synonymous_variant 0.13
rpoC 763675 c.306C>G synonymous_variant 0.1
rpoC 764485 c.1116G>C synonymous_variant 0.14
rpoC 764491 c.1122G>T synonymous_variant 0.13
rpoC 764497 c.1128A>G synonymous_variant 0.14
rpoC 764503 c.1134G>T synonymous_variant 0.14
rpoC 764509 c.1140G>C synonymous_variant 0.14
rpoC 764512 c.1143G>C synonymous_variant 0.14
rpoC 764521 c.1152T>C synonymous_variant 0.16
rpoC 764530 c.1161C>T synonymous_variant 0.17
rpoC 764536 c.1167G>C synonymous_variant 0.17
rpoC 764543 p.Thr392Ala missense_variant 0.19
rpoC 764548 c.1179G>C synonymous_variant 0.19
rpoC 764566 c.1197C>G synonymous_variant 0.25
rpoC 764573 p.Leu402Ile missense_variant 0.26
rpoC 764578 c.1209C>G synonymous_variant 0.27
rpoC 764581 c.1212T>C synonymous_variant 0.26
rpoC 764582 p.Leu405Met missense_variant 0.25
rpoC 764593 c.1224C>T synonymous_variant 0.35
rpoC 764602 c.1233C>T synonymous_variant 0.37
rpoC 764605 c.1236G>T synonymous_variant 0.37
rpoC 764611 c.1242G>T synonymous_variant 0.34
rpoC 764626 c.1257C>T synonymous_variant 0.3
rpoC 764632 c.1263T>C synonymous_variant 0.28
rpoC 764647 c.1278C>T synonymous_variant 0.26
rpoC 764650 c.1281G>C synonymous_variant 0.25
rpoC 764656 c.1287C>T synonymous_variant 0.29
rpoC 764662 c.1293G>C synonymous_variant 0.29
rpoC 764677 c.1308C>G synonymous_variant 0.29
rpoC 764678 p.Lys437Gln missense_variant 0.28
rpoC 764706 p.Leu446Gln missense_variant 0.27
rpoC 764713 c.1344G>T synonymous_variant 0.24
rpoC 764731 c.1362G>C synonymous_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.15
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.2
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.48
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.53
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.53
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.53
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.68
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.64
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.65
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.59
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.54
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.13
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.17
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.15
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.16
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.16
rrs 1472427 n.582T>G non_coding_transcript_exon_variant 0.16
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.16
rrs 1472436 n.591G>T non_coding_transcript_exon_variant 0.15
rrs 1472437 n.592T>G non_coding_transcript_exon_variant 0.14
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.14
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.13
rrs 1472449 n.604C>T non_coding_transcript_exon_variant 0.13
rrs 1472450 n.605A>C non_coding_transcript_exon_variant 0.13
rrs 1472451 n.606C>T non_coding_transcript_exon_variant 0.12
rrs 1472462 n.617T>G non_coding_transcript_exon_variant 0.19
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.19
rrs 1472473 n.628G>T non_coding_transcript_exon_variant 0.17
rrs 1472474 n.629C>G non_coding_transcript_exon_variant 0.16
rrs 1472476 n.631A>G non_coding_transcript_exon_variant 0.16
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.17
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.14
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.14
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.15
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.19
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.3
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.37
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.35
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.36
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.59
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.6
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.58
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.52
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.53
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.52
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.51
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.51
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.56
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.27
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.22
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.14
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.16
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.24
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.45
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.48
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.48
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.55
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.6
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.53
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.63
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.74
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.74
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.74
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.77
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.69
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.7
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.69
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.65
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.66
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.64
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.66
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 0.61
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.64
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.69
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.75
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.7
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.69
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.69
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.62
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.71
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.73
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.69
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.68
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.57
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.59
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.62
rrl 1473384 n.-274A>G upstream_gene_variant 0.21
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.18
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.1
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.1
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.13
rrl 1475038 n.1381G>C non_coding_transcript_exon_variant 0.17
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.39
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.55
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.56
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.59
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 0.59
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.62
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.49
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.51
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.52
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.52
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.55
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.55
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.51
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.55
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.5
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.49
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.49
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.49
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.42
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.35
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.32
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.21
rrl 1475995 n.2338G>C non_coding_transcript_exon_variant 0.21
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.22
rrl 1475998 n.2341C>G non_coding_transcript_exon_variant 0.22
rrl 1476000 n.2343G>A non_coding_transcript_exon_variant 0.24
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.24
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.7
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.76
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.78
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.77
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.8
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.7
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.46
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.21
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.17
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.14
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.14
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.14
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.18
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.12
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.12
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.12
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.19
rpsA 1833721 c.180A>G synonymous_variant 0.1
rpsA 1833727 c.186G>C synonymous_variant 0.1
rpsA 1833742 c.201A>G synonymous_variant 0.11
rpsA 1834195 c.654G>C synonymous_variant 0.14
rpsA 1834228 c.687C>T synonymous_variant 0.19
rpsA 1834234 c.693G>C synonymous_variant 0.17
rpsA 1834240 c.699T>C synonymous_variant 0.19
rpsA 1834246 c.705G>T synonymous_variant 0.22
rpsA 1834249 c.708T>C synonymous_variant 0.22
rpsA 1834261 c.720A>G synonymous_variant 0.22
rpsA 1834264 c.723G>C synonymous_variant 0.22
rpsA 1834294 c.753G>C synonymous_variant 0.32
rpsA 1834298 p.Gln253Glu missense_variant 0.32
rpsA 1834306 c.765T>C synonymous_variant 0.32
rpsA 1834307 p.Asp256Gln missense_variant 0.31
rpsA 1834312 c.771G>A synonymous_variant 0.3
rpsA 1834327 c.786G>T synonymous_variant 0.27
rpsA 1834345 c.804C>T synonymous_variant 0.23
rpsA 1834348 c.807T>C synonymous_variant 0.21
rpsA 1834354 c.813G>C synonymous_variant 0.19
rpsA 1834357 c.816T>C synonymous_variant 0.2
rpsA 1834360 c.819G>C synonymous_variant 0.18
rpsA 1834361 c.820T>C synonymous_variant 0.18
rpsA 1834366 c.825A>G synonymous_variant 0.18
rpsA 1834375 c.834G>C synonymous_variant 0.2
rpsA 1834378 c.837T>C synonymous_variant 0.21
rpsA 1834387 c.846C>T synonymous_variant 0.18
rpsA 1834411 c.870T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168412 p.Phe734Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246564 p.Leu17Phe missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0