TB-Profiler result

Run: ERR4815394
Summary

Run ID: ERR4815394

Sample name:

Date: 01-04-2023 13:50:21

Number of reads: 453359

Percentage reads mapped: 87.79

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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 0.12 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 0.12
rpoB 761051 c.1245G>C synonymous_variant 0.12
rpoB 761054 c.1248G>C synonymous_variant 0.12
rpoB 761057 c.1251G>C synonymous_variant 0.12
rpoB 761060 c.1254C>G synonymous_variant 0.13
rpoB 761084 c.1278C>A synonymous_variant 0.17
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.15
rpoB 761096 c.1290G>C synonymous_variant 0.13
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.13
rpoB 761102 c.1296A>G synonymous_variant 0.13
rpoB 761132 c.1326G>C synonymous_variant 0.12
rpoB 761133 c.1327T>C synonymous_variant 0.12
rpoB 761159 c.1353G>C synonymous_variant 0.11
rpoB 761165 c.1359G>C synonymous_variant 0.11
rpoB 761180 c.1374A>C synonymous_variant 0.11
rpoC 764485 c.1116G>C synonymous_variant 0.14
rpoC 764491 c.1122G>T synonymous_variant 0.12
rpoC 764497 c.1128A>G synonymous_variant 0.12
rpoC 764503 c.1134G>T synonymous_variant 0.12
rpoC 764509 c.1140G>C synonymous_variant 0.12
rpoC 764512 c.1143G>C synonymous_variant 0.12
rpoC 764521 c.1152T>C synonymous_variant 0.11
rpoC 764536 c.1167G>C synonymous_variant 0.12
rpoC 764543 p.Thr392Ala missense_variant 0.16
rpoC 764548 c.1179G>T synonymous_variant 0.16
rpoC 764566 c.1197C>G synonymous_variant 0.25
rpoC 764573 p.Leu402Ile missense_variant 0.23
rpoC 764578 c.1209C>G synonymous_variant 0.23
rpoC 764581 c.1212T>C synonymous_variant 0.22
rpoC 764582 p.Leu405Met missense_variant 0.22
rpoC 764602 c.1233C>T synonymous_variant 0.19
rpoC 764605 c.1236G>T synonymous_variant 0.19
rpoC 764611 c.1242G>T synonymous_variant 0.21
rpoC 764632 c.1263T>C synonymous_variant 0.17
rpoC 764647 c.1278C>T synonymous_variant 0.18
rpoC 764650 c.1281G>T synonymous_variant 0.18
rpoC 764653 c.1284G>C synonymous_variant 0.18
rpoC 764656 c.1287C>T synonymous_variant 0.18
rpoC 764662 c.1293G>C synonymous_variant 0.17
rpoC 764677 c.1308C>G synonymous_variant 0.17
rpoC 764678 p.Lys437Gln missense_variant 0.17
rpoC 766321 c.2953delA frameshift_variant 0.17
rpoC 766951 c.3582G>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460871 c.-174T>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.33
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.41
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.38
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.46
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.59
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.39
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.5
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.18
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.19
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.1
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.1
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.14
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.1
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.1
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.22
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.21
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.13
rrs 1472599 n.754G>T 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 0.23
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.23
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.25
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.17
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.22
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.22
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.2
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.16
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.16
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.28
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.28
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.28
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.25
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.32
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.32
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.32
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.37
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.33
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.35
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.36
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.38
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.38
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.3
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.27
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.32
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.26
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.32
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.32
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.32
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.27
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.29
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.3
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.31
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.3
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.28
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.28
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.35
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.41
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.42
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.41
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.38
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.32
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.34
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.13
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.12
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.11
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
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 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.37
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.37
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.36
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.41
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.15
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.11
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.11
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.12
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.12
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.13
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.17
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.17
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.17
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.11
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.11
inhA 1674648 c.447C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102401 c.642T>C synonymous_variant 1.0
PPE35 2168435 c.2178C>T synonymous_variant 0.11
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2222012 p.Gln385* stop_gained 1.0
Rv1979c 2222040 c.1125C>T synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.27
folC 2746669 p.Glu310Asp missense_variant 0.22
ald 3086742 c.-78A>C 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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246310 c.-204C>T upstream_gene_variant 1.0
embB 4248153 p.Ala547Val missense_variant 0.15
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0