TB-Profiler result

Run: ERR4407557
Summary

Run ID: ERR4407557

Sample name:

Date: 01-04-2023 05:49:51

Number of reads: 809448

Percentage reads mapped: 97.3

Strain: lineage4.2.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.1 Euro-American LAM7-TUR 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2288953 p.Gly97Cys missense_variant 1.0 pyrazinamide
pncA 2289113 c.128delA frameshift_variant 0.11 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326790 p.Trp228* stop_gained 0.12 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 5678 p.Ser147Pro missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7467 p.Leu56Ile missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8731 p.Gly477Val missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490633 c.-150C>G upstream_gene_variant 0.14
fgd1 490751 c.-32T>G upstream_gene_variant 0.22
fgd1 491243 p.Tyr154Cys missense_variant 0.33
mshA 575952 p.Gly202Glu missense_variant 0.13
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 620658 c.768C>A synonymous_variant 0.15
ccsA 620785 p.Gly299Arg missense_variant 0.13
rpoB 759615 c.-192A>C upstream_gene_variant 0.3
rpoB 761833 p.Thr676Ile missense_variant 0.12
rpoB 762308 c.2502G>A synonymous_variant 0.13
rpoB 762475 p.Gly890Val missense_variant 0.12
rpoB 762726 p.Ala974Thr missense_variant 0.13
rpoC 765260 p.Ala631Ser missense_variant 0.12
rpoC 765466 p.Asp699Glu missense_variant 0.18
rpoC 766679 p.His1104Tyr missense_variant 0.13
rpoC 767050 c.3681G>A synonymous_variant 0.2
rpoC 767255 p.Asp1296Tyr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776510 c.1971C>T synonymous_variant 0.13
mmpL5 777597 p.Arg295Gln missense_variant 0.18
mmpL5 778180 p.Leu101Phe missense_variant 0.15
mmpL5 778455 p.Pro9Leu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302780 c.-151G>T upstream_gene_variant 0.13
fbiC 1302807 c.-124G>A upstream_gene_variant 0.13
fbiC 1302812 c.-119G>T upstream_gene_variant 0.13
fbiC 1304108 p.Thr393Ile missense_variant 0.15
fbiC 1304931 c.2001C>T synonymous_variant 0.15
fbiC 1305037 p.Arg703Trp missense_variant 0.2
fbiC 1305174 c.2244T>C synonymous_variant 0.13
fbiC 1305308 p.Val793Ala missense_variant 0.18
fbiC 1305438 c.2508C>T synonymous_variant 0.18
embR 1416656 p.Val231Ala missense_variant 0.11
embR 1417046 p.Tyr101Phe missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.14
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.14
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.14
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.15
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.18
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.18
rrs 1473293 n.1448G>T non_coding_transcript_exon_variant 0.18
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.22
rrl 1475189 n.1532G>A non_coding_transcript_exon_variant 0.5
rrl 1476625 n.2968C>T non_coding_transcript_exon_variant 1.0
fabG1 1673158 c.-282C>A upstream_gene_variant 0.18
fabG1 1673206 c.-234C>G upstream_gene_variant 0.12
rpsA 1833442 c.-100G>T upstream_gene_variant 0.15
rpsA 1833480 c.-62G>T upstream_gene_variant 0.12
rpsA 1833602 p.Asp21His missense_variant 0.1
rpsA 1834758 p.Gly406Glu missense_variant 0.12
tlyA 1917849 c.-91G>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102726 p.His106Arg missense_variant 1.0
ndh 2102733 p.Leu104Ile missense_variant 0.12
ndh 2103013 c.30A>G synonymous_variant 0.1
katG 2154016 p.Gly699Glu missense_variant 0.12
katG 2155455 c.657G>A synonymous_variant 0.11
katG 2155471 p.Arg214Pro missense_variant 0.12
katG 2155856 p.Thr86Ala missense_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.11
PPE35 2167967 c.2646A>C synonymous_variant 0.11
PPE35 2168010 p.Ser868Asn missense_variant 0.11
PPE35 2168835 p.Pro593Leu missense_variant 0.11
PPE35 2169602 c.1011C>A synonymous_variant 0.12
PPE35 2170468 p.Thr49Pro missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289419 c.-178C>G upstream_gene_variant 0.15
pncA 2289811 c.-570C>A upstream_gene_variant 0.13
kasA 2518123 p.Gln3His missense_variant 0.1
kasA 2519161 c.1047G>A synonymous_variant 0.15
eis 2714284 p.Glu350Gly missense_variant 0.14
ahpC 2726014 c.-179A>G upstream_gene_variant 0.22
folC 2747097 p.Val168Ile missense_variant 0.12
folC 2747107 c.492G>T synonymous_variant 0.12
pepQ 2859919 p.Arg167Gln missense_variant 0.17
Rv2752c 3065075 p.Ser373Pro missense_variant 0.11
Rv2752c 3065424 c.768C>T synonymous_variant 0.17
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087090 p.Leu91Met missense_variant 0.11
fbiD 3339098 c.-20G>A upstream_gene_variant 0.25
Rv3083 3449032 p.Gly177Ser missense_variant 0.29
Rv3083 3449400 c.897C>G synonymous_variant 0.17
Rv3083 3449549 p.Asn349Ser missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611998 c.1119C>T synonymous_variant 0.17
Rv3236c 3612271 c.844_845delGT frameshift_variant 0.12
Rv3236c 3613212 c.-96C>T upstream_gene_variant 0.13
fbiB 3641921 c.387C>T synonymous_variant 0.12
fbiB 3642210 p.Gly226Ser missense_variant 0.25
alr 3840297 p.Thr375Met missense_variant 0.11
alr 3841111 p.Gly104Cys missense_variant 0.11
rpoA 3877749 c.759C>T synonymous_variant 1.0
rpoA 3877956 p.Glu184Asp missense_variant 1.0
rpoA 3878572 c.-65G>C upstream_gene_variant 1.0
ddn 3986817 c.-27C>T upstream_gene_variant 0.11
ddn 3987143 c.300A>T synonymous_variant 0.11
clpC1 4038727 p.Thr660Pro missense_variant 0.15
clpC1 4038910 p.Pro599Thr missense_variant 0.13
clpC1 4039374 p.Phe444Ser missense_variant 0.14
clpC1 4039682 c.1023C>T synonymous_variant 0.11
clpC1 4039691 c.1014G>C synonymous_variant 0.12
panD 4044456 c.-175T>G upstream_gene_variant 0.14
embC 4240559 p.Ala233Thr missense_variant 0.11
embC 4240847 p.Asp329Tyr missense_variant 0.12
embA 4242322 c.-911C>A upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244586 p.Leu452Met missense_variant 0.11
embA 4244621 c.1389G>A synonymous_variant 0.17
embB 4246613 p.Gly34Arg missense_variant 0.33
embB 4247098 c.585C>G synonymous_variant 0.15
embB 4248192 p.Arg560His missense_variant 0.12
embB 4248240 p.Gly576Val missense_variant 0.11
aftB 4268410 p.Leu143Met missense_variant 0.12
ethA 4327546 c.-73T>C upstream_gene_variant 0.13
ethA 4328354 c.-881T>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Ala missense_variant 1.0
gid 4408251 c.-49T>G upstream_gene_variant 0.13