TB-Profiler result

Run: SRR5535687
Summary

Run ID: SRR5535687

Sample name:

Date: 04-04-2023 10:37:48

Number of reads: 1705670

Percentage reads mapped: 99.33

Strain: lineage4.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.3 Euro-American T;X;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 761110 p.Asp435Val missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289073 p.His57Tyr missense_variant 1.0 pyrazinamide
pncA 2289235 p.Ala3Pro missense_variant 0.12 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407967 p.Leu79Ser missense_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
gyrB 5187 c.-53C>A upstream_gene_variant 0.13
gyrA 6304 c.-998C>A upstream_gene_variant 0.18
gyrB 7097 p.Glu620* stop_gained 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 1.0
fgd1 490860 c.79delG frameshift_variant 0.11
fgd1 491110 p.Ala110Ser missense_variant 0.11
fgd1 491754 p.Phe324Leu missense_variant 0.13
rpoB 763207 p.Ser1134Ile missense_variant 0.13
rpoC 763447 c.78C>A synonymous_variant 0.17
rpoC 764196 p.Ser276* stop_gained 0.13
rpoC 764438 p.Leu357Met missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767125 c.3756G>T synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776079 p.Ala801Asp missense_variant 0.21
mmpL5 776131 p.Leu784Ile missense_variant 0.14
mmpL5 776150 p.Met777Ile missense_variant 0.12
mmpL5 776767 p.Ala572Pro missense_variant 0.5
mmpR5 779144 p.Ser52Tyr missense_variant 0.12
mmpR5 779471 p.Thr161Ile missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.91
fbiC 1304610 c.1680C>T synonymous_variant 1.0
atpE 1461242 c.198C>A synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472007 n.162G>T non_coding_transcript_exon_variant 0.43
rrs 1472290 n.445C>A non_coding_transcript_exon_variant 0.18
rrs 1472391 n.546C>A non_coding_transcript_exon_variant 0.29
rrs 1473154 n.1309C>A non_coding_transcript_exon_variant 0.4
rrl 1473394 n.-264C>A upstream_gene_variant 0.3
rrl 1473718 n.61G>T non_coding_transcript_exon_variant 0.22
rrl 1474497 n.840G>T non_coding_transcript_exon_variant 0.29
rrl 1476714 n.3057G>C non_coding_transcript_exon_variant 0.25
fabG1 1673924 p.Gly162Val missense_variant 0.22
fabG1 1674058 p.Pro207Thr missense_variant 0.13
inhA 1674102 c.-100C>A upstream_gene_variant 0.2
inhA 1674450 c.249G>T synonymous_variant 0.2
inhA 1674719 p.Arg173Met missense_variant 0.13
rpsA 1833570 p.Gln10Arg missense_variant 0.11
rpsA 1833813 p.Leu91Arg missense_variant 0.14
rpsA 1833880 p.Trp113Cys missense_variant 0.12
rpsA 1834486 p.Glu315Asp missense_variant 0.22
rpsA 1834816 c.1275C>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102632 c.411C>A synonymous_variant 0.18
ndh 2103162 c.-120G>T upstream_gene_variant 0.13
PPE35 2168227 p.Thr796Ala missense_variant 0.22
Rv1979c 2221869 p.Tyr432* stop_gained 0.2
Rv1979c 2221885 p.Gly427Val missense_variant 0.2
Rv1979c 2222785 p.Trp127Leu missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289369 c.-128C>A upstream_gene_variant 0.17
pncA 2289657 c.-416G>T upstream_gene_variant 0.14
eis 2714263 p.Gly357Asp missense_variant 0.15
ahpC 2726233 p.Gln14Arg missense_variant 0.13
folC 2747566 c.33G>T synonymous_variant 0.13
Rv2752c 3064629 c.1563C>A synonymous_variant 0.14
Rv2752c 3065512 p.Arg227Gln missense_variant 1.0
Rv2752c 3065892 p.Ile100Met missense_variant 0.14
thyA 3074215 p.Asp86Val missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448956 c.453G>A synonymous_variant 0.15
Rv3083 3449465 p.Ile321Thr missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474135 c.129G>A synonymous_variant 0.18
Rv3236c 3612936 p.Gly61Ser missense_variant 0.15
fbiB 3642863 c.1329T>C synonymous_variant 0.11
clpC1 4039071 p.Pro545Leu missense_variant 0.17
clpC1 4039540 p.Tyr389Asp missense_variant 0.11
clpC1 4039882 p.Glu275* stop_gained 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249211 p.Leu900Phe missense_variant 0.12
aftB 4266969 p.Pro623Gln missense_variant 0.18
aftB 4266971 c.1866C>T synonymous_variant 0.18
aftB 4268005 c.832T>C synonymous_variant 0.13
aftB 4268641 p.Leu66Met missense_variant 0.18
ubiA 4269382 p.Cys151Phe missense_variant 0.18
ethA 4327067 p.Leu136Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407596 p.Val203Met missense_variant 0.11