TB-Profiler result

Run: ERR4829816
Summary

Run ID: ERR4829816

Sample name:

Date: 01-04-2023 19:42:11

Number of reads: 3036259

Percentage reads mapped: 86.36

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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 0.19 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761037 c.1231T>C synonymous_variant 0.1
rpoB 761051 c.1245G>C synonymous_variant 0.11
rpoB 761054 c.1248G>C synonymous_variant 0.11
rpoB 761057 c.1251G>C synonymous_variant 0.13
rpoB 761060 c.1254C>G synonymous_variant 0.13
rpoB 761084 c.1278C>A synonymous_variant 0.13
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.13
rpoB 761096 c.1290G>C synonymous_variant 0.15
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.15
rpoB 761102 c.1296A>G synonymous_variant 0.19
rpoB 761123 c.1317G>C synonymous_variant 0.15
rpoB 761126 c.1320G>C synonymous_variant 0.14
rpoB 761132 c.1326G>C synonymous_variant 0.14
rpoB 761133 c.1327T>C synonymous_variant 0.14
rpoB 761150 c.1344A>T synonymous_variant 0.14
rpoB 761159 c.1353G>C synonymous_variant 0.2
rpoB 761165 c.1359G>T synonymous_variant 0.15
rpoB 762080 c.2274G>C synonymous_variant 0.1
rpoB 762085 p.Ala760Glu missense_variant 0.12
rpoB 762089 c.2283G>A synonymous_variant 0.13
rpoB 762114 p.Ile770Val missense_variant 0.12
rpoB 762134 c.2328C>T synonymous_variant 0.14
rpoB 762143 c.2337T>C synonymous_variant 0.16
rpoB 762149 c.2343G>C synonymous_variant 0.16
rpoB 762156 p.Val784Ile missense_variant 0.16
rpoB 762167 c.2361T>C synonymous_variant 0.17
rpoB 762176 c.2370T>C synonymous_variant 0.17
rpoB 762177 p.Arg791Thr missense_variant 0.14
rpoB 762181 p.Asp792Ala missense_variant 0.17
rpoB 762185 c.2379G>C synonymous_variant 0.18
rpoB 762194 c.2388G>C synonymous_variant 0.17
rpoB 762200 c.2394C>T synonymous_variant 0.15
rpoB 762224 c.2418C>T synonymous_variant 0.12
rpoC 763589 p.Ile74Val missense_variant 0.11
rpoC 763642 c.273G>C synonymous_variant 0.16
rpoC 763648 c.279C>T synonymous_variant 0.13
rpoC 763657 p.Glu96Asp missense_variant 0.16
rpoC 763660 c.291T>G synonymous_variant 0.19
rpoC 763666 c.297G>C synonymous_variant 0.22
rpoC 763699 c.330G>T synonymous_variant 0.16
rpoC 763714 c.345G>C synonymous_variant 0.19
rpoC 763717 c.348T>C synonymous_variant 0.15
rpoC 763718 p.Leu117Val missense_variant 0.14
rpoC 763723 c.354G>C synonymous_variant 0.12
rpoC 763729 c.360G>C synonymous_variant 0.11
rpoC 763732 c.363C>G synonymous_variant 0.12
rpoC 763751 p.Ile128Val missense_variant 0.21
rpoC 763772 p.Val135Met missense_variant 0.16
rpoC 764581 c.1212T>C synonymous_variant 0.1
rpoC 764611 c.1242G>T synonymous_variant 0.12
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 1472108 n.263C>T non_coding_transcript_exon_variant 0.44
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.16
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.42
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.42
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.42
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.15
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.57
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.42
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.42
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.17
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.2
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.15
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.17
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.11
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.42
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.31
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.29
rrs 1472685 n.840G>T non_coding_transcript_exon_variant 0.13
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.23
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.24
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.23
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.26
rrs 1472701 n.856T>C non_coding_transcript_exon_variant 0.12
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.27
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.32
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.24
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.12
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.13
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.2
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.28
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.37
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.39
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.26
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.34
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.53
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.51
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.51
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.53
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.15
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.22
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.39
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.34
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.16
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.31
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.15
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.16
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.31
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.3
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.31
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.35
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.23
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.21
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.41
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.34
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.3
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.3
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.41
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.38
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.42
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.37
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.34
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.21
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.26
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.29
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.34
rrl 1474628 n.971C>T non_coding_transcript_exon_variant 0.11
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.14
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.19
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.12
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.12
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.16
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.16
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.11
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.13
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.13
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.11
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.12
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.14
rrl 1476032 n.2375C>G non_coding_transcript_exon_variant 0.14
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.14
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.14
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.12
rrl 1476046 n.2389G>C non_coding_transcript_exon_variant 0.12
rrl 1476047 n.2390G>C non_coding_transcript_exon_variant 0.12
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.12
rrl 1476058 n.2401T>C non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.48
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.45
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
rpsA 1834231 c.690T>C synonymous_variant 0.12
rpsA 1834234 c.693G>C synonymous_variant 0.13
rpsA 1834240 c.699T>C synonymous_variant 0.13
rpsA 1834246 c.705G>T synonymous_variant 0.12
rpsA 1834249 c.708T>C synonymous_variant 0.14
rpsA 1834261 c.720A>G synonymous_variant 0.19
rpsA 1834264 c.723G>C synonymous_variant 0.17
rpsA 1834294 c.753G>C synonymous_variant 0.23
rpsA 1834298 p.Gln253Glu missense_variant 0.23
rpsA 1834306 c.765T>C synonymous_variant 0.21
rpsA 1834307 p.Asp256Gln missense_variant 0.2
rpsA 1834312 c.771G>A synonymous_variant 0.21
rpsA 1834327 c.786G>T synonymous_variant 0.2
rpsA 1834345 c.804C>T synonymous_variant 0.17
rpsA 1834348 c.807T>C synonymous_variant 0.18
rpsA 1834354 c.813G>C synonymous_variant 0.17
rpsA 1834357 c.816T>C synonymous_variant 0.17
rpsA 1834360 c.819G>C synonymous_variant 0.17
rpsA 1834361 c.820T>C synonymous_variant 0.16
rpsA 1834366 c.825A>G synonymous_variant 0.16
rpsA 1834375 c.834G>C synonymous_variant 0.16
rpsA 1834378 c.837T>C synonymous_variant 0.14
rpsA 1834387 c.846C>T synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2222074 p.Pro364Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065999 p.Arg65Ser missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0