TB-Profiler result

Run: ERR4872096
Summary

Run ID: ERR4872096

Sample name:

Date: 01-04-2023 21:21:52

Number of reads: 5284711

Percentage reads mapped: 91.77

Strain: lineage4.6.2.2

Drug-resistance: MDR-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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.2 Euro-American T;LAM RD726 0.99
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 761155 p.Ser450Leu missense_variant 0.94 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2289225 p.Ile6Thr missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.98 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 8129 c.828T>C synonymous_variant 0.13
gyrA 8135 c.834C>G synonymous_variant 0.14
gyrA 8177 c.876A>C synonymous_variant 0.13
gyrA 8189 c.888G>C synonymous_variant 0.14
gyrA 8198 c.897T>C synonymous_variant 0.14
gyrA 8207 c.906T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>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 1472108 n.263C>T non_coding_transcript_exon_variant 0.13
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.2
rrl 1474043 n.386G>A non_coding_transcript_exon_variant 0.21
rrl 1474091 n.436G>T non_coding_transcript_exon_variant 0.24
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.19
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.18
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.26
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.26
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.16
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.16
rrl 1475028 n.1371G>A non_coding_transcript_exon_variant 0.15
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.18
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.2
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.27
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.22
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.24
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.24
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.21
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.21
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.17
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.18
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.19
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.33
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.14
inhA 1673393 c.-809G>C upstream_gene_variant 1.0
rpsA 1834249 c.708T>C synonymous_variant 0.13
rpsA 1834348 c.807T>C synonymous_variant 0.14
rpsA 1834357 c.816T>G synonymous_variant 0.14
rpsA 1834528 c.987T>C synonymous_variant 0.13
rpsA 1834540 c.999G>T synonymous_variant 0.14
rpsA 1834546 c.1005T>C synonymous_variant 0.14
rpsA 1834555 c.1014T>G synonymous_variant 0.15
rpsA 1834609 c.1068T>C synonymous_variant 0.13
rpsA 1834639 c.1098T>C synonymous_variant 0.13
rpsA 1834666 c.1125G>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154980 p.Leu378Met missense_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746320 p.Pro427Ala missense_variant 0.99
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
ddn 3987011 c.168C>T synonymous_variant 1.0
clpC1 4039409 c.1296T>C synonymous_variant 0.13
clpC1 4039412 c.1293T>G synonymous_variant 0.13
clpC1 4039415 p.Glu430Asp missense_variant 0.13
clpC1 4039430 c.1275T>C synonymous_variant 0.14
clpC1 4039454 c.1251A>G synonymous_variant 0.13
clpC1 4039466 c.1239T>C synonymous_variant 0.15
clpC1 4039469 c.1236T>C synonymous_variant 0.14
clpC1 4039481 c.1224T>C synonymous_variant 0.15
clpC1 4039484 c.1221T>C synonymous_variant 0.13
clpC1 4039517 c.1188C>G synonymous_variant 0.15
clpC1 4039589 c.1116G>T synonymous_variant 0.13
clpC1 4039622 c.1083C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embB 4246584 p.Arg24Pro missense_variant 0.28
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0