TB-Profiler result

Run: SRR5535696
Summary

Run ID: SRR5535696

Sample name:

Date: 04-04-2023 10:38:13

Number of reads: 1956647

Percentage reads mapped: 99.4

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.97
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 761110 p.Asp435Val missense_variant 1.0 rifampicin
mmpR5 779402 p.Glu138Gly missense_variant 0.2 clofazimine, bedaquiline
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326780 c.693dupG frameshift_variant 1.0 ethionamide, ethionamide
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
gyrB 5520 p.Pro94Leu missense_variant 0.18
gyrB 5541 p.Thr101Lys missense_variant 0.12
gyrB 6124 c.885C>A synonymous_variant 0.22
gyrA 6685 c.-617C>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 0.96
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491660 p.Ala293Asp missense_variant 0.12
mshA 575152 c.-196G>A upstream_gene_variant 0.17
ccsA 620535 p.Met215Ile missense_variant 0.22
rpoB 759827 p.Ser7Arg missense_variant 0.19
rpoB 759889 p.Gly28Val missense_variant 0.2
rpoB 759891 p.Ala29Ser missense_variant 0.2
rpoB 761045 c.1239C>T synonymous_variant 0.22
rpoC 763530 p.Pro54Leu missense_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765652 p.Gln761His missense_variant 0.12
rpoC 766752 p.Arg1128His missense_variant 0.25
mmpL5 775619 c.2862G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778938 c.-458G>T upstream_gene_variant 0.13
mmpL5 779448 c.-968G>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781875 p.Gly106Cys missense_variant 0.15
rplC 800813 p.Ala2Val missense_variant 0.18
fbiC 1303432 p.Asp168Tyr missense_variant 0.14
fbiC 1303741 p.Ala271Ser missense_variant 0.14
fbiC 1304448 c.1518C>A synonymous_variant 0.13
fbiC 1304541 c.1611C>A synonymous_variant 0.3
Rv1258c 1406395 p.Val316Met missense_variant 0.12
Rv1258c 1406510 c.831G>T synonymous_variant 0.14
Rv1258c 1407319 p.Pro8Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471910 n.65T>C non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 1.0
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 1.0
rrl 1473693 n.36G>T non_coding_transcript_exon_variant 0.29
rrl 1474134 n.477G>T non_coding_transcript_exon_variant 0.67
rrl 1474432 n.775C>A non_coding_transcript_exon_variant 0.67
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 1.0
fabG1 1673575 p.His46Asn missense_variant 0.33
fabG1 1673771 p.Ala111Asp missense_variant 0.33
inhA 1673781 c.-421C>T upstream_gene_variant 0.29
inhA 1674235 p.Val12Phe missense_variant 0.17
inhA 1674257 p.Ser19Leu missense_variant 0.18
inhA 1674797 p.Met199Arg missense_variant 0.14
rpsA 1833978 p.Gly146Val missense_variant 0.15
rpsA 1834025 p.Gln162* stop_gained 0.17
rpsA 1834397 p.His286Asn missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103012 p.Pro11Thr missense_variant 0.17
katG 2154157 p.Ser652* stop_gained 0.2
katG 2154807 c.1305C>A synonymous_variant 0.14
katG 2155260 c.852C>A synonymous_variant 0.18
katG 2156350 c.-239C>A upstream_gene_variant 0.18
PPE35 2167658 c.2955C>A synonymous_variant 0.14
PPE35 2168558 c.2055C>A synonymous_variant 0.17
PPE35 2169317 p.Phe432Leu missense_variant 0.17
PPE35 2169516 p.Ser366Tyr missense_variant 0.13
PPE35 2170026 p.Pro196Leu missense_variant 0.15
Rv1979c 2221732 p.Pro478Gln missense_variant 0.18
Rv1979c 2222717 p.Ala150Ser missense_variant 0.4
Rv1979c 2222802 c.363C>A synonymous_variant 0.15
Rv1979c 2222846 p.Gly107Trp missense_variant 0.15
Rv1979c 2222951 p.Val72Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518216 c.102G>A synonymous_variant 0.15
kasA 2518592 p.Ala160Ser missense_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714260 p.Ser358Ile missense_variant 0.2
eis 2715510 c.-178G>C upstream_gene_variant 0.12
ahpC 2726684 c.492G>T synonymous_variant 0.25
pepQ 2860297 p.Gly41Asp missense_variant 0.13
pepQ 2860594 c.-176C>A upstream_gene_variant 0.15
Rv2752c 3064950 c.1242C>T synonymous_variant 0.14
thyX 3067498 p.Leu150Met missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074665 c.-194A>G upstream_gene_variant 0.22
ald 3086713 c.-107C>A upstream_gene_variant 0.18
ald 3086769 c.-51A>C upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448623 c.120C>A synonymous_variant 0.18
Rv3083 3449000 p.Pro166Gln missense_variant 0.14
Rv3083 3449400 c.897C>A synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474318 c.312C>A synonymous_variant 0.2
fprA 3474507 c.501C>A synonymous_variant 0.17
fprA 3474984 c.978G>T synonymous_variant 0.23
Rv3236c 3612451 c.666G>T synonymous_variant 0.22
fbiA 3640579 p.Ala13Pro missense_variant 0.29
alr 3840437 c.984G>T synonymous_variant 0.15
rpoA 3877640 p.Gly290Ser missense_variant 0.13
rpoA 3877650 p.Ile286Met missense_variant 0.12
rpoA 3878421 c.86delG frameshift_variant 0.14
ddn 3986698 c.-146C>A upstream_gene_variant 0.14
ddn 3986812 c.-32T>A upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038794 p.Ser637Arg missense_variant 0.15
clpC1 4039214 p.Phe497Leu missense_variant 0.27
clpC1 4039282 p.Val475Leu missense_variant 0.2
clpC1 4039784 c.921C>A synonymous_variant 0.17
clpC1 4039802 c.903G>A synonymous_variant 0.22
clpC1 4040485 p.Pro74Thr missense_variant 0.14
clpC1 4040598 p.Gly36Val missense_variant 0.14
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243532 c.300C>A synonymous_variant 0.14
embA 4244607 p.Leu459Val missense_variant 0.1
embB 4245896 c.-618C>T upstream_gene_variant 0.18
embB 4248739 c.2226G>A synonymous_variant 0.18
aftB 4267044 p.Thr598Asn missense_variant 0.2
aftB 4267134 p.Cys568Phe missense_variant 0.29
aftB 4267586 c.1251C>G synonymous_variant 0.31
aftB 4268686 p.Gln51Lys missense_variant 0.14
ubiA 4269355 p.Arg160Leu missense_variant 0.2
ubiA 4269714 p.Leu40Phe missense_variant 0.19
ethA 4327320 p.Gly52* stop_gained 0.18
ethR 4327591 p.Arg15Val missense_variant 0.15
ethA 4327770 c.-297G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0