TB-Profiler result

Run: SRR4035832
Summary

Run ID: SRR4035832

Sample name:

Date: 04-04-2023 07:19:36

Number of reads: 918878

Percentage reads mapped: 99.43

Strain: lineage4.1.2

Drug-resistance: Other

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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 0.99
lineage4.1.2 Euro-American T;H None 0.99
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 7566 p.Asp89Asn missense_variant 0.25 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 5529 p.Asp97Val missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7365 c.65delA frameshift_variant 0.17
gyrA 7388 c.87C>T synonymous_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8949 p.Lys550Glu missense_variant 0.18
gyrA 9055 p.Pro585Leu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491234 p.Asp151Gly missense_variant 0.29
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575973 p.Glu209Val missense_variant 0.14
mshA 576450 p.Pro368Leu missense_variant 0.25
mshA 576578 p.Gly411Trp missense_variant 0.2
ccsA 620166 c.276G>C synonymous_variant 0.12
ccsA 620435 p.Gly182Asp missense_variant 0.33
ccsA 620731 p.Ala281Thr missense_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760147 p.Asp114Gly missense_variant 0.11
rpoB 760441 p.Lys212Arg missense_variant 0.18
rpoB 762627 p.Asp941Tyr missense_variant 0.15
rpoB 763068 p.Asp1088Asn missense_variant 0.5
rpoB 763099 p.Glu1098Val missense_variant 0.4
rpoB 763107 p.Val1101Ile missense_variant 0.33
rpoB 763135 p.Gly1110Ala missense_variant 0.25
rpoB 763161 p.Leu1119Ile missense_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764706 p.Leu446Pro missense_variant 0.12
rpoC 764708 p.Met447Leu missense_variant 0.12
rpoC 765057 p.Asn563Ile missense_variant 0.13
rpoC 765078 p.Ser570Phe missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765884 p.Ser839Pro missense_variant 0.12
rpoC 765956 p.Thr863Ser missense_variant 0.15
rpoC 766090 c.2721C>T synonymous_variant 0.13
rpoC 766290 p.Val974Glu missense_variant 0.17
rpoC 766303 c.2934C>T synonymous_variant 0.2
rpoC 766316 p.Met983Val missense_variant 0.25
rpoC 766323 p.Thr985Ile missense_variant 0.22
rpoC 767092 c.3723C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776995 p.Ser496Pro missense_variant 0.11
mmpL5 777280 p.Ala401Pro missense_variant 0.12
mmpL5 777289 p.Val398Met missense_variant 0.13
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpR5 779038 p.Met17Val missense_variant 0.12
mmpR5 779141 p.Gln51Leu missense_variant 0.14
mmpR5 779341 p.Ala118Thr missense_variant 0.18
mmpR5 779354 p.Leu122Pro missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781410 c.-150G>A upstream_gene_variant 0.18
rplC 800636 c.-173C>T upstream_gene_variant 0.13
fbiC 1302956 p.Ser9Phe missense_variant 0.12
fbiC 1303147 p.Ala73Thr missense_variant 0.14
fbiC 1303571 p.Met214Thr missense_variant 0.13
fbiC 1303588 p.Arg220* stop_gained 0.13
fbiC 1304012 p.Thr361Met missense_variant 0.17
fbiC 1304360 p.Arg477His missense_variant 0.15
fbiC 1304504 p.Leu525Gln missense_variant 0.25
fbiC 1304774 p.Ala615Val missense_variant 0.16
Rv1258c 1407053 c.288C>T synonymous_variant 0.13
embR 1416496 c.852G>C synonymous_variant 0.13
embR 1416521 p.Val276Ala missense_variant 0.13
embR 1416758 p.Leu197Gln missense_variant 0.18
embR 1416938 p.His137Arg missense_variant 0.14
embR 1417140 p.Ala70Thr missense_variant 0.13
embR 1417155 p.Pro65Thr missense_variant 0.12
embR 1417332 p.Thr6Ser missense_variant 0.18
embR 1417507 c.-160A>T upstream_gene_variant 0.14
atpE 1461263 c.219G>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471961 n.116C>T non_coding_transcript_exon_variant 0.14
rrs 1472143 n.298G>T non_coding_transcript_exon_variant 0.13
rrs 1472440 n.595G>A non_coding_transcript_exon_variant 0.12
rrs 1472448 n.603T>A non_coding_transcript_exon_variant 0.13
rrs 1472456 n.611T>C non_coding_transcript_exon_variant 0.13
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.14
rrs 1473155 n.1310A>G non_coding_transcript_exon_variant 0.1
rrl 1473590 n.-68A>T upstream_gene_variant 0.18
rrl 1473599 n.-59T>C upstream_gene_variant 0.2
rrl 1473605 n.-53G>C upstream_gene_variant 0.2
rrl 1473617 n.-41T>C upstream_gene_variant 0.2
rrl 1473997 n.340T>A non_coding_transcript_exon_variant 0.22
rrl 1475689 n.2032T>C non_coding_transcript_exon_variant 0.11
rrl 1475879 n.2222T>C non_coding_transcript_exon_variant 0.12
rrl 1476437 n.2780A>T non_coding_transcript_exon_variant 0.15
rrl 1476701 n.3044A>G non_coding_transcript_exon_variant 0.11
fabG1 1674038 p.Gln200Leu missense_variant 0.17
inhA 1674668 p.Pro156Leu missense_variant 0.25
inhA 1674803 p.Ala201Glu missense_variant 0.15
rpsA 1833895 c.354G>A synonymous_variant 0.33
rpsA 1833982 p.Phe147Leu missense_variant 0.15
rpsA 1834240 c.699T>A synonymous_variant 0.15
rpsA 1834248 p.His236Leu missense_variant 0.17
rpsA 1834459 c.918G>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918041 c.102C>A synonymous_variant 0.18
katG 2154422 p.Thr564Ala missense_variant 0.13
katG 2154575 p.Asp513Asn missense_variant 0.12
katG 2155936 p.Gly59Val missense_variant 0.12
PPE35 2168927 c.1686G>T synonymous_variant 0.13
PPE35 2169616 p.Asn333Asp missense_variant 0.15
PPE35 2170288 p.Leu109Met missense_variant 0.13
PPE35 2170304 c.309G>T synonymous_variant 0.13
Rv1979c 2222348 p.Val273Ile missense_variant 0.15
Rv1979c 2222429 p.Asp246His missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290093 c.-852G>A upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519340 p.Val409Glu missense_variant 0.18
eis 2714347 p.Phe329Tyr missense_variant 0.15
eis 2714355 c.978C>T synonymous_variant 0.2
eis 2714362 p.Ser324Phe missense_variant 0.18
ahpC 2726461 p.Glu90Gly missense_variant 0.12
ahpC 2726727 p.Arg179Cys missense_variant 0.17
folC 2746192 c.1407C>T synonymous_variant 0.15
folC 2746612 c.987C>G synonymous_variant 0.2
folC 2746815 p.Glu262Lys missense_variant 0.22
pepQ 2859366 p.Met351Ile missense_variant 0.15
pepQ 2859419 p.Gly334Arg missense_variant 0.14
pepQ 2859594 c.825T>A synonymous_variant 0.12
pepQ 2860251 c.168C>G synonymous_variant 0.25
ribD 2986759 c.-80C>T upstream_gene_variant 0.17
ribD 2987273 c.435C>A synonymous_variant 0.15
ribD 2987491 p.Tyr218Cys missense_variant 0.2
Rv2752c 3064765 p.Thr476Ile missense_variant 0.14
Rv2752c 3065455 p.Gln246Arg missense_variant 0.13
Rv2752c 3065478 p.Phe238Leu missense_variant 0.15
Rv2752c 3065534 p.Pro220Thr missense_variant 0.18
Rv2752c 3065899 p.Pro98Leu missense_variant 0.13
Rv2752c 3065901 c.291A>G synonymous_variant 0.13
Rv2752c 3067096 c.-905C>A upstream_gene_variant 0.18
thyX 3067394 c.552G>T synonymous_variant 0.14
thyX 3068146 c.-201T>A upstream_gene_variant 0.14
thyA 3073691 p.Val261Leu missense_variant 0.11
thyA 3073747 c.724delA frameshift_variant 0.2
thyA 3073965 p.Asp169Glu missense_variant 0.17
thyA 3074308 p.Val55Ala missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086789 c.-31A>G upstream_gene_variant 0.13
ald 3087527 c.708T>C synonymous_variant 0.11
ald 3087820 p.Arg334Pro missense_variant 0.13
fbiD 3339336 c.219C>T synonymous_variant 0.22
fbiD 3339432 c.315_316insT frameshift_variant 0.25
fbiD 3339442 p.Asn109Asp missense_variant 0.2
fbiD 3339690 c.573C>A synonymous_variant 0.18
Rv3083 3448750 p.Gln83* stop_gained 0.2
Rv3083 3449277 c.774C>T synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474008 c.2T>C start_lost 0.13
fprA 3474273 p.Gln89His missense_variant 0.17
fprA 3474351 c.345C>G synonymous_variant 0.2
fprA 3474799 p.Arg265Ser missense_variant 0.2
fprA 3474916 p.Ala304Pro missense_variant 0.29
whiB7 3568498 p.Glu61Gly missense_variant 0.18
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612645 p.Glu158* stop_gained 0.2
Rv3236c 3613128 c.-12A>G upstream_gene_variant 0.27
fbiA 3640921 p.Gln127Glu missense_variant 0.11
fbiA 3640928 p.Thr129Ile missense_variant 0.12
fbiB 3641286 c.-249C>T upstream_gene_variant 0.2
fbiA 3641390 p.Gly283Ala missense_variant 0.17
fbiB 3641942 c.408G>A synonymous_variant 0.22
fbiB 3641991 p.Gly153Arg missense_variant 0.17
fbiB 3642621 p.Ala363Thr missense_variant 0.18
alr 3840349 p.Ala358Thr missense_variant 0.18
alr 3840411 p.Gly337Asp missense_variant 0.17
alr 3841187 c.234C>T synonymous_variant 0.12
rpoA 3877878 c.630G>A synonymous_variant 0.18
rpoA 3877963 p.Arg182Gln missense_variant 0.15
rpoA 3878072 p.Tyr146His missense_variant 0.13
clpC1 4038312 p.Gln798Arg missense_variant 0.18
clpC1 4038964 p.Asp581Tyr missense_variant 0.2
clpC1 4038975 p.Leu577His missense_variant 0.18
clpC1 4039000 p.Phe569Ile missense_variant 0.17
clpC1 4039590 p.Val372Ala missense_variant 0.17
clpC1 4040612 p.Glu31Asp missense_variant 0.15
clpC1 4040641 p.Met22Val missense_variant 0.12
clpC1 4040726 c.-22G>A upstream_gene_variant 0.14
panD 4044236 p.Thr16Ala missense_variant 0.12
embC 4239998 p.Ala46Thr missense_variant 0.13
embC 4240730 p.Asn290Asp missense_variant 0.22
embC 4240773 p.Ser304Phe missense_variant 0.13
embC 4241543 p.Ala561Thr missense_variant 0.18
embC 4241837 p.Trp659Arg missense_variant 0.15
embC 4242039 p.Ala726Val missense_variant 0.15
embC 4242047 p.Ser729Thr missense_variant 0.15
embC 4242134 p.Glu758* stop_gained 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243178 c.-55C>A upstream_gene_variant 0.22
embA 4244080 p.Val283Asp missense_variant 0.29
embA 4244786 c.1554G>A synonymous_variant 0.17
embA 4245129 p.Pro633Ser missense_variant 0.14
embA 4245302 c.2070G>A synonymous_variant 0.29
embA 4245471 c.2241delC frameshift_variant 0.29
embB 4248885 p.Asn791Ser missense_variant 0.11
aftB 4267232 p.Asp535Glu missense_variant 0.11
aftB 4267326 p.Val504Gly missense_variant 0.22
aftB 4267924 p.Val305Met missense_variant 0.2
aftB 4268103 p.Ala245Val missense_variant 0.15
ubiA 4269596 p.Ala80Thr missense_variant 0.5
ethA 4326115 c.1359A>G synonymous_variant 0.13
ethA 4326682 p.Phe264Leu missense_variant 0.12
ethR 4327132 c.-417G>A upstream_gene_variant 0.17
ethA 4327458 p.Asp6Tyr missense_variant 0.18
ethA 4327465 p.Glu3Asp missense_variant 0.18
ethR 4327976 p.Gln143Arg missense_variant 0.17
ethR 4328161 p.His205Asp missense_variant 0.17
ethA 4328246 c.-773C>T upstream_gene_variant 0.18
whiB6 4338186 c.336T>G synonymous_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407959 p.Ala82Pro missense_variant 0.11
gid 4408106 p.Arg33Trp missense_variant 0.18