TB-Profiler result

Run: SRR3732593
Summary

Run ID: SRR3732593

Sample name:

Date: 04-04-2023 05:36:22

Number of reads: 1237647

Percentage reads mapped: 99.52

Strain: lineage4.1.2.1

Drug-resistance: HR-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
lineage4.1.2 Euro-American T;H None 0.88
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.8
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
katG 2154877 p.Trp412* stop_gained 0.12 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 6289 c.1050C>A synonymous_variant 0.12
gyrB 7032 p.Gly598Glu missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.81
gyrA 8440 p.Arg380Leu missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 0.9
fgd1 490982 p.Arg67Pro missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 0.86
fgd1 491610 c.828A>G synonymous_variant 0.15
mshA 575283 c.-65C>A upstream_gene_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 0.9
ccsA 620075 p.Gly62Val missense_variant 0.2
ccsA 620095 p.His69Tyr missense_variant 0.18
ccsA 620465 p.Ala192Asp missense_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 0.67
rpoB 760555 p.Glu250Gly missense_variant 1.0
rpoB 762437 p.Asp877Glu missense_variant 0.12
rpoB 763064 p.Lys1086Asn missense_variant 0.2
rpoC 763706 p.Arg113Trp missense_variant 0.13
rpoC 763855 c.486C>T synonymous_variant 0.15
rpoC 764212 c.843C>A synonymous_variant 0.15
rpoC 764960 p.Ala531Ser missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.78
rpoC 766762 p.Gln1131His missense_variant 0.15
rpoC 767071 c.3702C>A synonymous_variant 0.15
rpoC 767302 c.3933C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775841 c.2640G>A synonymous_variant 0.15
mmpL5 776909 p.Glu524Asp missense_variant 0.17
mmpL5 777119 p.His454Gln missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777310 p.Gly391Cys missense_variant 0.15
mmpL5 777545 c.936C>A synonymous_variant 0.13
mmpL5 777886 p.Ala199Ser missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302920 c.-11G>A upstream_gene_variant 0.67
fbiC 1303620 c.690C>T synonymous_variant 0.17
fbiC 1304101 p.Arg391Trp missense_variant 0.12
fbiC 1304834 p.Pro635Gln missense_variant 0.13
fbiC 1304896 p.Leu656Met missense_variant 0.15
fbiC 1305077 p.Pro716Gln missense_variant 0.17
Rv1258c 1406621 c.720G>A synonymous_variant 0.14
Rv1258c 1406909 c.432C>A synonymous_variant 0.14
embR 1416907 c.441G>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475168 n.1511G>A non_coding_transcript_exon_variant 0.29
rrl 1476375 n.2718C>A non_coding_transcript_exon_variant 0.33
rrl 1476397 n.2740G>T non_coding_transcript_exon_variant 0.5
fabG1 1673534 p.Ala32Glu missense_variant 0.15
inhA 1674304 p.Gln35Glu missense_variant 0.18
inhA 1674916 p.Ala239Ser missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918532 p.Val198Asp missense_variant 0.15
tlyA 1918564 p.Leu209Ile missense_variant 0.2
ndh 2102244 p.Arg267Trp missense_variant 0.18
katG 2155738 p.Gly125Val missense_variant 0.18
katG 2155942 p.Pro57Gln missense_variant 0.12
katG 2156370 c.-259T>A upstream_gene_variant 0.17
katG 2156448 c.-337C>A upstream_gene_variant 0.33
katG 2156559 c.-448C>A upstream_gene_variant 0.25
PPE35 2167658 c.2955C>A synonymous_variant 0.13
PPE35 2168149 p.Pro822Ser missense_variant 0.21
PPE35 2170136 c.477G>T synonymous_variant 0.2
PPE35 2170687 c.-75C>T upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.75
eis 2715577 c.-245G>A upstream_gene_variant 0.13
folC 2746277 p.Asp441Gly missense_variant 0.87
folC 2747537 p.Pro21Leu missense_variant 0.33
pepQ 2860283 p.Phe46Leu missense_variant 0.24
pepQ 2860545 c.-127G>T upstream_gene_variant 0.13
Rv2752c 3064580 p.Gly538Ser missense_variant 0.13
Rv2752c 3064763 p.Val477Phe missense_variant 0.14
Rv2752c 3064985 p.Leu403Met missense_variant 0.11
Rv2752c 3065398 p.Ser265* stop_gained 0.18
Rv2752c 3065439 c.753C>A synonymous_variant 0.12
Rv2752c 3065584 p.Ser203Leu missense_variant 0.22
Rv2752c 3066254 c.-63G>A upstream_gene_variant 0.2
thyA 3073762 p.Ser237* stop_gained 0.25
thyA 3074016 c.456C>T synonymous_variant 0.25
thyA 3074504 c.-33T>C upstream_gene_variant 0.17
ald 3086755 c.-65C>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087896 c.1077G>T synonymous_variant 0.13
fbiD 3338960 c.-158C>A upstream_gene_variant 0.12
fbiD 3338997 c.-121C>A upstream_gene_variant 0.15
fbiD 3339258 p.Leu47Phe missense_variant 0.15
Rv3083 3448456 c.-48G>T upstream_gene_variant 0.22
Rv3083 3448519 p.Asp6His missense_variant 0.5
Rv3083 3449198 p.Arg232His missense_variant 0.29
Rv3083 3449644 p.Ala381Thr missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.81
whiB7 3568504 p.Arg59Gln missense_variant 0.13
Rv3236c 3612640 p.Asp159Glu missense_variant 0.2
rpoA 3877477 p.Thr344Asn missense_variant 0.17
rpoA 3878036 p.Glu158Lys missense_variant 0.12
ddn 3986741 c.-103C>A upstream_gene_variant 0.17
ddn 3987099 p.Pro86Ser missense_variant 0.12
clpC1 4038341 p.Lys788Asn missense_variant 0.22
clpC1 4039042 p.Ser555Thr missense_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 0.4
clpC1 4039898 c.807C>T synonymous_variant 0.12
panD 4044350 c.-69C>A upstream_gene_variant 0.12
embC 4239847 c.-16C>A upstream_gene_variant 0.12
embC 4240570 c.708C>A synonymous_variant 0.2
embC 4241113 c.1251G>A synonymous_variant 0.13
embC 4241834 p.Arg658* stop_gained 0.12
embC 4242267 p.Arg802His missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.93
embA 4243963 p.Val244Ala missense_variant 0.2
embA 4244108 p.Asn292Lys missense_variant 0.13
embA 4244769 p.Gly513Trp missense_variant 0.13
embA 4245172 p.Thr647Lys missense_variant 0.17
embA 4245282 p.Ile684Val missense_variant 0.15
embB 4247975 p.Val488Phe missense_variant 0.12
embB 4248397 p.Phe628Leu missense_variant 0.12
aftB 4268649 p.Trp63Leu missense_variant 0.13
ubiA 4269889 c.-56C>A upstream_gene_variant 0.15
ubiA 4269893 c.-60G>T upstream_gene_variant 0.15
ethA 4326924 p.Gly184Cys missense_variant 0.14
ethR 4327260 c.-289G>T upstream_gene_variant 0.12
ethA 4327471 c.3G>T start_lost 0.22
ethR 4327573 p.Ala9Thr missense_variant 0.22
ethR 4327824 p.Glu92Asp missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407781 p.Ala141Glu missense_variant 0.22