TB-Profiler result

Run: ERR1950084
Summary

Run ID: ERR1950084

Sample name:

Date: 31-03-2023 15:39:24

Number of reads: 359207

Percentage reads mapped: 99.17

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 5640 p.Arg134Leu missense_variant 0.2
gyrB 6270 p.Asn344Thr missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8749 p.Leu483His missense_variant 0.25
gyrA 9550 p.Val750Gly missense_variant 0.33
fgd1 491008 p.Thr76Pro missense_variant 0.29
fgd1 491232 p.Phe150Leu missense_variant 0.5
mshA 575293 c.-55T>G upstream_gene_variant 0.3
mshA 575711 p.Lys122* stop_gained 0.22
mshA 576561 c.1215delG frameshift_variant 0.15
mshA 576574 p.Cys409Trp missense_variant 0.18
ccsA 619702 c.-189C>G upstream_gene_variant 0.5
ccsA 620748 c.858T>G synonymous_variant 0.33
rpoB 759676 c.-131A>T upstream_gene_variant 0.5
rpoB 759727 c.-80A>T upstream_gene_variant 0.5
rpoB 760542 p.Phe246Ile missense_variant 0.43
rpoB 761073 p.Glu423* stop_gained 0.33
rpoB 761197 p.Leu464Arg missense_variant 0.25
rpoB 761596 p.Asn597Thr missense_variant 0.18
rpoB 762324 p.Lys840* stop_gained 0.29
rpoB 762382 p.Val859Ala missense_variant 0.22
rpoC 763944 p.Asp192Ala missense_variant 0.18
rpoC 764973 p.Asp535Ala missense_variant 0.29
rpoC 765776 p.Val803Ile missense_variant 0.22
rpoC 766098 p.Leu910Arg missense_variant 0.29
rpoC 766348 p.Glu993Asp missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775996 p.Ile829Phe missense_variant 0.4
mmpL5 776443 p.Phe680Val missense_variant 0.33
mmpL5 776847 p.Gln545Leu missense_variant 0.29
mmpL5 776917 p.Met522Leu missense_variant 0.29
mmpL5 776952 p.Leu510Gln missense_variant 0.4
mmpL5 778047 p.Lys145Met missense_variant 0.38
mmpL5 778078 p.Thr135Pro missense_variant 0.5
mmpL5 779103 c.-623T>A upstream_gene_variant 0.5
mmpR5 779440 p.Ser151Thr missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781674 p.Thr39Pro missense_variant 0.38
rplC 801249 c.441T>G synonymous_variant 0.38
fbiC 1302996 c.66T>C synonymous_variant 0.33
fbiC 1303038 c.108T>C synonymous_variant 0.33
fbiC 1305104 p.Val725Ala missense_variant 0.18
Rv1258c 1406206 p.Thr379Ala missense_variant 0.5
Rv1258c 1406987 c.354G>A synonymous_variant 0.29
embR 1417128 p.Ser74Thr missense_variant 0.22
embR 1417465 c.-118A>G upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472354 n.509C>A non_coding_transcript_exon_variant 0.17
rrs 1472608 n.763T>A non_coding_transcript_exon_variant 0.29
rrs 1472676 n.831C>A non_coding_transcript_exon_variant 0.2
rrs 1472743 n.898T>G non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474017 n.360A>T non_coding_transcript_exon_variant 0.5
rrl 1474226 n.569A>T non_coding_transcript_exon_variant 0.25
rrl 1474331 n.674A>T non_coding_transcript_exon_variant 0.22
rrl 1474935 n.1278A>G non_coding_transcript_exon_variant 0.33
rrl 1475035 n.1378A>T non_coding_transcript_exon_variant 0.67
rrl 1475050 n.1393A>T non_coding_transcript_exon_variant 0.4
rrl 1475556 n.1899A>T non_coding_transcript_exon_variant 0.43
rrl 1475812 n.2155T>A non_coding_transcript_exon_variant 0.25
rrl 1476088 n.2431A>T non_coding_transcript_exon_variant 0.5
rrl 1476757 n.3100T>A non_coding_transcript_exon_variant 0.5
fabG1 1674089 p.Val217Gly missense_variant 0.4
inhA 1674892 p.Asn231Tyr missense_variant 0.25
rpsA 1833742 p.Glu67Asp missense_variant 0.33
rpsA 1833840 p.Leu100Arg missense_variant 0.33
rpsA 1834498 c.957C>A synonymous_variant 0.67
rpsA 1834505 p.His322Asn missense_variant 0.67
rpsA 1834518 p.Leu326Arg missense_variant 0.5
tlyA 1917915 c.-25T>G upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918013 p.Glu25Val missense_variant 0.25
tlyA 1918252 p.Ala105Ser missense_variant 0.22
ndh 2102321 p.Val241Ala missense_variant 0.33
ndh 2103077 c.-35G>A upstream_gene_variant 0.5
katG 2154866 p.Ile416Leu missense_variant 0.67
PPE35 2167859 c.2754T>G synonymous_variant 0.5
PPE35 2168195 c.2418G>T synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168869 p.Pro582Thr missense_variant 0.2
PPE35 2169352 p.Ala421Thr missense_variant 0.33
PPE35 2169875 p.Asn246Lys missense_variant 0.33
PPE35 2170022 c.591T>G synonymous_variant 0.33
PPE35 2170047 p.Leu189Arg missense_variant 0.6
PPE35 2170178 c.435T>G synonymous_variant 0.43
PPE35 2170436 c.177T>G synonymous_variant 0.17
Rv1979c 2222631 c.534T>A synonymous_variant 0.4
Rv1979c 2222864 p.Thr101Ser missense_variant 0.4
Rv1979c 2222971 p.Phe65Tyr missense_variant 0.38
Rv1979c 2223084 c.81A>T synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289232 p.Leu4Val missense_variant 0.25
kasA 2518903 c.789C>A synonymous_variant 0.29
kasA 2518943 p.Met277Leu missense_variant 0.25
kasA 2519128 c.1014G>C synonymous_variant 0.18
kasA 2519131 c.1017G>C synonymous_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.22
kasA 2519143 c.1029G>C synonymous_variant 0.22
kasA 2519346 p.Leu411Arg missense_variant 0.57
eis 2714138 p.Ala399Thr missense_variant 0.29
eis 2714905 p.Asp143Ala missense_variant 0.67
eis 2715321 c.12C>A synonymous_variant 0.2
ahpC 2726108 c.-85A>T upstream_gene_variant 0.2
ahpC 2726160 c.-33A>T upstream_gene_variant 0.18
ahpC 2726303 c.111T>A synonymous_variant 0.3
pepQ 2860249 p.Asp57Ala missense_variant 0.4
pepQ 2860498 c.-80A>G upstream_gene_variant 0.67
ribD 2987053 p.Asn72Thr missense_variant 0.5
ribD 2987290 p.Asp151Ala missense_variant 0.43
Rv2752c 3064918 p.Asn425Ile missense_variant 0.4
Rv2752c 3065183 p.Ser337Thr missense_variant 0.33
Rv2752c 3065356 p.Leu279Gln missense_variant 0.67
Rv2752c 3065867 p.Leu109Met missense_variant 0.67
thyX 3068157 c.-212T>G upstream_gene_variant 0.29
thyA 3074543 c.-72T>G upstream_gene_variant 1.0
ald 3086887 p.Val23Gly missense_variant 0.22
ald 3087010 p.Val64Gly missense_variant 0.22
ald 3087382 p.Asn188Ser missense_variant 0.4
fbiD 3339386 p.Asp90Val missense_variant 0.4
fprA 3474247 p.Asn81Tyr missense_variant 0.29
fprA 3474418 p.Phe138Ile missense_variant 0.25
fprA 3474986 p.Val327Gly missense_variant 0.5
Rv3236c 3612531 p.Phe196Val missense_variant 0.4
fbiA 3640441 c.-102T>A upstream_gene_variant 0.29
fbiA 3640763 p.Asp74Ala missense_variant 0.17
fbiB 3641596 p.Pro21His missense_variant 0.5
fbiB 3641953 p.Leu140Arg missense_variant 0.5
fbiB 3642181 p.Val216Gly missense_variant 0.4
alr 3840583 p.Ala280Ser missense_variant 0.33
alr 3840852 p.Leu190Arg missense_variant 0.43
alr 3841122 p.Leu100Arg missense_variant 0.4
alr 3841376 c.45A>T synonymous_variant 0.25
alr 3841595 c.-175T>A upstream_gene_variant 0.33
rpoA 3877473 p.Glu345Asp missense_variant 1.0
ddn 3986943 p.Gly34Arg missense_variant 0.29
clpC1 4038753 p.Gln651Arg missense_variant 0.22
clpC1 4040249 p.Glu152Asp missense_variant 0.33
panD 4044209 p.Ser25Ala missense_variant 0.36
embC 4240733 p.Thr291Pro missense_variant 0.5
embC 4240890 p.Trp343Leu missense_variant 0.25
embC 4241803 c.1941T>A synonymous_variant 0.33
embC 4242204 p.Leu781Gln missense_variant 0.67
embC 4242240 p.Asp793Ala missense_variant 1.0
embC 4242252 p.Asp797Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244197 p.Val322Gly missense_variant 0.25
embA 4245421 p.Leu730Arg missense_variant 0.5
embA 4246291 p.Leu1020Gln missense_variant 0.33
embB 4247336 p.Thr275Ala missense_variant 0.5
embB 4247460 p.Met316Lys missense_variant 0.5
embB 4247597 c.1086delG frameshift_variant 0.29
aftB 4267062 p.Leu592* stop_gained 0.4
aftB 4268769 p.Gln23Arg missense_variant 0.67
aftB 4268952 c.-116G>A upstream_gene_variant 0.33
ubiA 4269327 p.Lys169Asn missense_variant 0.5
ubiA 4269800 p.Asn12Tyr missense_variant 0.5
ethA 4326059 p.Lys472Met missense_variant 0.29
ethA 4327203 p.Met91Leu missense_variant 0.25
ethA 4327386 p.Lys30* stop_gained 0.4
ethR 4327813 p.Thr89Pro missense_variant 0.5
ethA 4327911 c.-438G>T upstream_gene_variant 0.29
whiB6 4338286 p.Val79Gly missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0