TB-Profiler result

Run: SRR4035763
Summary

Run ID: SRR4035763

Sample name:

Date: 04-04-2023 07:17:04

Number of reads: 1433503

Percentage reads mapped: 99.51

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.2 Euro-American T;H 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 761155 p.Ser450Leu missense_variant 0.18 rifampicin
katG 2154921 p.Trp397* stop_gained 0.22 isoniazid
katG 2155458 p.Asn218Lys missense_variant 0.13 isoniazid
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 5657 p.Lys140Glu missense_variant 0.13
gyrA 6781 c.-521C>T upstream_gene_variant 0.2
gyrB 7217 p.Arg660Cys missense_variant 0.15
gyrB 7223 p.Phe662Ile missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7786 p.Glu162Val missense_variant 0.14
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8159 c.859delA frameshift_variant 0.14
gyrA 8242 p.Ile314Asn missense_variant 0.15
gyrA 8691 p.Asp464Tyr missense_variant 0.25
gyrA 9232 p.Arg644His missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9315 c.2014C>T synonymous_variant 0.17
gyrA 9328 p.Ala676Val missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576302 c.955C>T synonymous_variant 0.14
mshA 576346 c.999C>T synonymous_variant 0.14
mshA 576611 p.Ala422Thr missense_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761203 p.Val466Ala missense_variant 0.11
rpoB 762313 p.Gly836Asp missense_variant 0.2
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764551 c.1182G>T synonymous_variant 0.17
rpoC 764563 c.1194G>C synonymous_variant 0.17
rpoC 765025 p.Gln552His missense_variant 0.17
rpoC 765071 p.Pro568Ser missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 0.94
rpoC 765490 c.2121C>T synonymous_variant 0.14
rpoC 766493 p.Gly1042Cys missense_variant 0.12
rpoC 766587 p.Glu1073Gly missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpS5 778683 p.Asp75Tyr missense_variant 0.15
mmpS5 779488 c.-583A>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781479 c.-80_-79delAC upstream_gene_variant 0.13
rplC 800698 c.-111A>G upstream_gene_variant 0.11
rplC 800811 c.3G>C start_lost 0.12
rplC 800840 p.Leu11Pro missense_variant 0.12
Rv1258c 1406646 p.Asp232Gly missense_variant 0.11
embR 1416611 p.Thr246Arg missense_variant 0.11
atpE 1460936 c.-109T>G upstream_gene_variant 0.11
atpE 1460938 c.-107C>G upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474323 n.666C>T non_coding_transcript_exon_variant 0.17
rrl 1474335 n.678T>A non_coding_transcript_exon_variant 0.18
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.17
rrl 1475401 n.1744A>G non_coding_transcript_exon_variant 0.33
inhA 1673718 c.-484G>A upstream_gene_variant 0.14
inhA 1674759 c.558G>C synonymous_variant 0.11
inhA 1674827 p.Glu209Gly missense_variant 0.13
inhA 1674933 c.732G>A synonymous_variant 0.15
rpsA 1834301 c.762delT frameshift_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918377 c.438T>C synonymous_variant 0.12
ndh 2102475 p.Ala190Thr missense_variant 0.15
ndh 2103240 c.-198C>T upstream_gene_variant 0.12
katG 2154836 p.Tyr426His missense_variant 0.2
katG 2155264 p.Leu283Pro missense_variant 0.13
PPE35 2168766 p.Ser616Ile missense_variant 0.12
PPE35 2168877 p.Phe579Ser missense_variant 0.18
Rv1979c 2222746 p.Thr140Arg missense_variant 0.22
Rv1979c 2222795 p.Asp124Asn missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519047 c.933C>T synonymous_variant 0.12
ahpC 2726383 p.Glu64Gly missense_variant 0.22
folC 2746194 p.Thr469Ala missense_variant 0.11
folC 2747421 p.Pro60Ser missense_variant 0.12
ribD 2987209 p.Gly124Ala missense_variant 0.11
thyX 3067623 p.Tyr108Phe missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339323 p.Ala69Val missense_variant 0.15
Rv3083 3448951 c.448C>T synonymous_variant 0.12
Rv3083 3449039 p.Lys179Met missense_variant 0.14
Rv3083 3449093 p.Ala197Val missense_variant 0.17
Rv3083 3449109 c.606C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475366 p.Gly454Arg missense_variant 0.18
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
fbiB 3640558 c.-977C>T upstream_gene_variant 0.18
fbiA 3640689 p.Asp49Glu missense_variant 0.11
alr 3840652 p.Val257Met missense_variant 0.14
alr 3840684 p.Leu246Pro missense_variant 0.11
alr 3841045 p.Ala126Pro missense_variant 0.1
rpoA 3878602 c.-95G>C upstream_gene_variant 0.22
ddn 3986993 c.150C>G synonymous_variant 0.1
clpC1 4040187 p.Gln173Arg missense_variant 0.18
panD 4044147 c.135C>A synonymous_variant 0.15
embC 4240067 p.Ser69Gly missense_variant 0.11
embC 4240130 p.Ala90Thr missense_variant 0.14
embC 4242419 p.Ser853Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242858 p.His999Arg missense_variant 0.13
embA 4245968 c.2738delC frameshift_variant 0.12
embB 4249263 p.Val917Ala missense_variant 0.12
aftB 4267823 c.1014G>A synonymous_variant 0.12
ethA 4328222 c.-749G>C upstream_gene_variant 0.17
ethA 4328233 c.-760G>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0