TB-Profiler result

Run: SRR18337382
Summary

Run ID: SRR18337382

Sample name:

Date: 03-04-2023 19:37:16

Number of reads: 922247

Percentage reads mapped: 99.45

Strain: lineage4.1.2.1

Drug-resistance: HR-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
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
katG 2155168 p.Ser315Thr missense_variant 0.92 isoniazid
katG 2155991 c.120delC frameshift_variant 0.12 isoniazid
ethA 4326066 c.1407delG frameshift_variant 0.1 ethionamide, 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 5637 p.Thr133Ile missense_variant 0.11
gyrB 7017 p.Ala593Val missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7378 p.Arg26His missense_variant 0.14
gyrA 7432 p.Val44Glu missense_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7750 p.Val150Ala missense_variant 0.14
gyrA 7952 c.651C>T synonymous_variant 0.14
gyrA 8499 p.Ala400Ser missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9653 c.2352C>T synonymous_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491683 p.Val301Leu missense_variant 0.22
fgd1 491741 p.Phe320Tyr missense_variant 0.22
mshA 575572 p.Ser75Arg missense_variant 0.11
mshA 575679 p.Asn111Ser missense_variant 0.94
mshA 575916 p.Asp190Val missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.21
mshA 576111 p.Ala255Gly missense_variant 0.18
mshA 576295 c.948C>T synonymous_variant 0.12
mshA 576493 c.1146C>G synonymous_variant 0.33
ccsA 619783 c.-108C>G upstream_gene_variant 0.15
ccsA 620312 p.Leu141Pro missense_variant 0.12
ccsA 620746 p.Gly286Arg missense_variant 0.1
rpoB 759954 p.Val50Ile missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761495 c.1689G>A synonymous_variant 0.12
rpoB 761655 c.1853delC frameshift_variant 0.2
rpoB 761687 c.1882_1887delGCGGCG conservative_inframe_deletion 0.17
rpoB 761949 p.Val715Leu missense_variant 0.14
rpoB 762000 p.Ser732Pro missense_variant 0.11
rpoC 762506 c.-864C>T upstream_gene_variant 0.25
rpoB 762549 p.Gly915Ser missense_variant 0.2
rpoC 763405 p.Ile12Met missense_variant 0.25
rpoC 763745 p.Glu126Lys missense_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765307 c.1939delG frameshift_variant 0.17
rpoC 765483 p.Pro705Gln missense_variant 0.17
rpoC 766081 c.2712T>C synonymous_variant 0.11
rpoC 767187 p.Gln1273Pro missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776092 p.Ser797Gly missense_variant 0.17
mmpL5 776844 p.Met546Arg missense_variant 0.17
mmpL5 776856 c.1624delC frameshift_variant 0.11
mmpL5 777074 c.1407C>T synonymous_variant 0.15
mmpL5 777757 p.Ala242Thr missense_variant 1.0
mmpR5 778298 c.-692C>A upstream_gene_variant 0.13
mmpS5 778673 p.Pro78Gln missense_variant 0.12
mmpS5 779557 c.-652A>T upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303214 p.Thr95Ile missense_variant 0.17
fbiC 1303486 p.Gly186Trp missense_variant 0.12
fbiC 1303958 p.Cys343Phe missense_variant 0.1
fbiC 1303992 p.Trp354* stop_gained 0.12
fbiC 1305340 p.Ala804Thr missense_variant 0.14
Rv1258c 1406525 c.816G>T synonymous_variant 0.2
Rv1258c 1406598 p.Pro248Leu missense_variant 0.12
Rv1258c 1406964 p.Ser126* stop_gained 0.12
Rv1258c 1406988 p.Pro118Arg missense_variant 0.15
embR 1416214 p.Phe378Leu missense_variant 0.29
embR 1416293 p.Val352Glu missense_variant 0.17
embR 1416645 c.700_702delACA conservative_inframe_deletion 0.2
embR 1416687 p.Gln221* stop_gained 0.12
embR 1417519 c.-172C>T upstream_gene_variant 0.17
atpE 1461278 c.234A>C synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472731 n.886C>T non_coding_transcript_exon_variant 0.14
rrl 1474126 n.469G>A non_coding_transcript_exon_variant 0.25
rrl 1474492 n.839_852delCGGGTAAGACCGCG non_coding_transcript_exon_variant 1.0
rrl 1476542 n.2885T>G non_coding_transcript_exon_variant 0.17
fabG1 1674013 p.Arg192Gly missense_variant 0.25
inhA 1674615 p.Met138Ile missense_variant 0.2
rpsA 1833795 p.Glu85Val missense_variant 0.17
rpsA 1834338 p.Asp266Gly missense_variant 0.11
tlyA 1917840 c.-100C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918081 p.Asp48Asn missense_variant 0.1
ndh 2101741 c.1293_1301delCACCGACCA disruptive_inframe_deletion 0.11
ndh 2101905 c.1126_1137delTTTTCGGCGGTG conservative_inframe_deletion 0.13
ndh 2102151 p.Asp298Tyr missense_variant 0.2
ndh 2102987 p.Ile19Thr missense_variant 0.17
katG 2154010 p.Asn701Ser missense_variant 0.12
katG 2154363 c.1749C>A synonymous_variant 0.12
katG 2154700 p.Gln471Arg missense_variant 0.1
katG 2154823 p.Leu430Pro missense_variant 0.2
katG 2154909 c.1203C>G synonymous_variant 0.14
katG 2155265 c.847C>T synonymous_variant 0.1
katG 2156278 c.-167T>G upstream_gene_variant 0.2
PPE35 2167721 c.2892C>G synonymous_variant 0.12
PPE35 2167792 p.Ser941Ala missense_variant 1.0
PPE35 2168083 p.Ile844Leu missense_variant 0.17
PPE35 2168111 c.2502C>T synonymous_variant 0.18
PPE35 2168927 c.1686G>T synonymous_variant 0.14
Rv1979c 2222304 c.861C>T synonymous_variant 0.17
Rv1979c 2222741 p.Leu142Phe missense_variant 0.14
Rv1979c 2223212 c.-48A>G upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289237 p.Arg2Gln missense_variant 0.4
pncA 2289299 c.-58T>G upstream_gene_variant 0.14
pncA 2289381 c.-140C>T upstream_gene_variant 0.15
pncA 2289494 c.-253A>C upstream_gene_variant 0.2
pncA 2290105 c.-864G>T upstream_gene_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518648 c.534C>T synonymous_variant 0.2
kasA 2518877 p.Lys255Gln missense_variant 0.14
kasA 2519046 p.His311Arg missense_variant 0.13
eis 2714553 c.780C>T synonymous_variant 0.25
eis 2714581 p.Ala251Val missense_variant 0.25
ahpC 2726577 p.Gly129Arg missense_variant 0.12
ahpC 2726703 p.Asp171His missense_variant 0.17
folC 2746983 p.Gly206Ser missense_variant 0.12
folC 2747078 p.Glu174Arg missense_variant 0.17
folC 2747171 p.Gly143Asp missense_variant 0.11
folC 2747199 p.Ile134Val missense_variant 0.12
pepQ 2860206 c.213C>T synonymous_variant 0.12
pepQ 2860250 p.Asp57Tyr missense_variant 0.2
pepQ 2860254 c.165C>T synonymous_variant 0.2
pepQ 2860411 p.His3Pro missense_variant 0.14
ribD 2986860 p.Gly8* stop_gained 0.17
Rv2752c 3064806 c.1386G>A synonymous_variant 0.11
Rv2752c 3064858 c.1327_1333delCCGGTGG frameshift_variant 0.18
Rv2752c 3065455 p.Gln246Pro missense_variant 0.14
Rv2752c 3065539 p.Val218Ala missense_variant 0.14
Rv2752c 3065760 c.432C>T synonymous_variant 0.14
Rv2752c 3065775 p.Phe139Leu missense_variant 0.14
Rv2752c 3067025 c.-834G>A upstream_gene_variant 0.12
thyX 3067568 c.378C>T synonymous_variant 0.13
thyX 3067692 p.Ile85Thr missense_variant 0.14
thyA 3074029 p.Ala148Gly missense_variant 0.11
thyA 3074155 p.Gly106Val missense_variant 0.14
thyA 3074312 p.Ser54Ala missense_variant 0.15
thyA 3074613 c.-142C>T upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087185 c.366C>A synonymous_variant 0.17
ald 3087280 p.Gly154Val missense_variant 0.15
ald 3087735 p.Pro306Thr missense_variant 0.17
fbiD 3339428 p.Ala104Asp missense_variant 0.12
Rv3083 3448469 c.-35A>G upstream_gene_variant 0.15
Rv3083 3449907 c.1404G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612187 p.Met310Ile missense_variant 0.2
Rv3236c 3612673 c.444G>A synonymous_variant 0.2
rpoA 3878334 c.174T>C synonymous_variant 0.14
ddn 3986979 p.Val46Phe missense_variant 0.17
clpC1 4039021 c.1684C>T synonymous_variant 0.15
clpC1 4039197 p.Glu503Gly missense_variant 0.14
panD 4043863 c.419A>C stop_lost&splice_region_variant 0.33
embC 4239712 c.-151T>C upstream_gene_variant 0.2
embC 4239792 c.-71G>C upstream_gene_variant 0.14
embC 4239833 c.-30G>C upstream_gene_variant 0.2
embC 4240867 c.1005T>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242781 c.2924_2926delTGG disruptive_inframe_deletion 0.11
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243011 p.Lys1050Arg missense_variant 0.17
embA 4244082 p.Ala284Pro missense_variant 0.17
embA 4245316 p.Val695Ala missense_variant 0.17
embB 4246575 p.Ala21Val missense_variant 0.25
embB 4246679 p.Leu56Phe missense_variant 0.11
embB 4246809 p.Leu99Arg missense_variant 0.2
embB 4247033 p.Ser174Gly missense_variant 0.22
embB 4247437 c.924A>G synonymous_variant 0.13
embB 4247477 p.Trp322Arg missense_variant 0.12
embB 4247765 c.1252C>T synonymous_variant 0.25
embB 4247770 c.1258delG frameshift_variant 0.33
embB 4248055 c.1542G>T synonymous_variant 0.25
embB 4248102 p.Leu530Pro missense_variant 0.13
embB 4248956 c.2446delG frameshift_variant 0.5
embB 4249321 c.2808A>G synonymous_variant 0.33
embB 4249422 p.Asp970Val missense_variant 0.14
embB 4249480 c.2967G>A synonymous_variant 0.12
embB 4249617 p.Gly1035Asp missense_variant 0.17
aftB 4267200 p.Trp546Pro missense_variant 0.25
aftB 4267771 c.1066T>C synonymous_variant 0.11
aftB 4268967 c.-131G>C upstream_gene_variant 0.25
aftB 4268988 c.-152G>C upstream_gene_variant 0.33
ubiA 4269888 c.-55C>T upstream_gene_variant 0.13
ethA 4327126 p.Trp116Cys missense_variant 0.11
whiB6 4338194 p.Arg110Trp missense_variant 0.13
whiB6 4338488 p.Cys12Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407966 p.Leu79Phe missense_variant 0.12
gid 4408146 c.16_56delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT frameshift_variant 1.0