TB-Profiler result

Run: SRR4035795
Summary

Run ID: SRR4035795

Sample name:

Date: 04-04-2023 07:18:12

Number of reads: 824605

Percentage reads mapped: 99.46

Strain: lineage4.1.2

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
lineage4.1.2 Euro-American T;H 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
katG 2155165 p.Gly316Asp missense_variant 0.18 isoniazid
ethA 4326426 c.1047delT frameshift_variant 0.14 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 5667 p.Gly143Ala missense_variant 0.18
gyrB 7202 p.Asp655Tyr missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7418 c.117C>T synonymous_variant 0.33
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8173 p.Val291Asp missense_variant 0.14
gyrA 8182 p.Gly294Asp missense_variant 0.15
gyrA 8283 c.983delT frameshift_variant 0.18
gyrA 9056 c.1755C>T synonymous_variant 0.15
gyrA 9059 p.Glu586Asp missense_variant 0.15
gyrA 9078 p.Gly593Arg missense_variant 0.17
gyrA 9156 p.Asp619Tyr missense_variant 0.29
gyrA 9200 c.1899A>G synonymous_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9390 p.Thr697Ala missense_variant 0.25
fgd1 490700 c.-83G>A upstream_gene_variant 0.13
fgd1 491054 p.Ala91Val missense_variant 0.15
fgd1 491171 p.Ala130Gly missense_variant 0.15
fgd1 491391 c.609C>T synonymous_variant 0.33
fgd1 491483 p.Ser234Tyr missense_variant 0.25
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491678 p.Gln299Arg missense_variant 0.17
mshA 575311 c.-37A>T upstream_gene_variant 0.17
mshA 575379 p.Gly11Glu missense_variant 0.14
mshA 575842 c.495G>A synonymous_variant 0.2
ccsA 619839 c.-52C>T upstream_gene_variant 0.15
ccsA 620017 p.Gly43Arg missense_variant 0.2
ccsA 620027 p.Pro46Gln missense_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760436 c.630C>T synonymous_variant 0.15
rpoB 760443 p.Arg213Cys missense_variant 0.2
rpoB 760860 p.Pro352Thr missense_variant 0.15
rpoB 761172 p.Gly456Cys missense_variant 0.25
rpoB 761535 p.Pro577Ser missense_variant 0.2
rpoB 762364 p.Asp853Val missense_variant 0.15
rpoC 763552 c.183C>T synonymous_variant 0.17
rpoC 763592 p.Cys75Ser missense_variant 0.18
rpoC 764024 c.655T>C synonymous_variant 0.14
rpoC 764104 c.735C>G synonymous_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764922 p.Glu518Val missense_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765922 c.2555delA frameshift_variant 0.17
rpoC 766498 p.Lys1043Asn missense_variant 0.18
rpoC 766848 p.Gln1160Arg missense_variant 0.17
rpoC 766900 c.3531T>C synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776025 p.Ser819Leu missense_variant 0.17
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 778360 p.Val41Ile missense_variant 0.22
mmpR5 779233 p.Arg82Trp missense_variant 0.22
mmpR5 779285 p.Ala99Val missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801272 p.Ala155Val missense_variant 0.29
rplC 801442 p.Ile212Phe missense_variant 0.14
rplC 801452 p.Gly215Asp missense_variant 0.15
fbiC 1302827 c.-104A>G upstream_gene_variant 0.14
fbiC 1303190 p.Ser87Leu missense_variant 0.13
fbiC 1303308 c.378C>T synonymous_variant 0.14
fbiC 1303697 p.Thr256Ile missense_variant 0.33
fbiC 1304147 p.Ile406Asn missense_variant 0.25
fbiC 1304216 c.1289delC frameshift_variant 0.33
fbiC 1304721 c.1791C>T synonymous_variant 0.13
fbiC 1304748 c.1821delC frameshift_variant 0.15
fbiC 1304820 c.1890G>A synonymous_variant 0.29
fbiC 1304835 c.1905G>A synonymous_variant 0.4
Rv1258c 1406548 p.Met265Val missense_variant 0.25
Rv1258c 1407276 p.Gly22Asp missense_variant 0.12
embR 1416870 p.Glu160Gln missense_variant 0.15
embR 1416882 p.Phe156Ile missense_variant 0.17
embR 1416900 p.Leu150Val missense_variant 0.18
embR 1416923 p.Leu142Ser missense_variant 0.22
atpE 1461049 p.Asp2Gly missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471904 n.59T>C non_coding_transcript_exon_variant 0.2
rrs 1471918 n.73A>G non_coding_transcript_exon_variant 0.15
rrs 1472545 n.700A>G non_coding_transcript_exon_variant 0.5
rrs 1472873 n.1028C>A non_coding_transcript_exon_variant 0.33
rrl 1474020 n.363A>G non_coding_transcript_exon_variant 0.29
rrl 1475077 n.1420C>A non_coding_transcript_exon_variant 0.25
fabG1 1673319 c.-121A>T upstream_gene_variant 0.25
inhA 1674307 p.Leu36Val missense_variant 0.17
inhA 1674670 p.Ala157Thr missense_variant 0.17
inhA 1674871 p.Gln224Lys missense_variant 0.17
rpsA 1833401 c.-141C>A upstream_gene_variant 0.2
rpsA 1834063 p.Ile174Met missense_variant 0.12
rpsA 1834592 p.Ile351Val missense_variant 0.13
rpsA 1834818 p.Lys426Arg missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918183 p.Ala82Ser missense_variant 0.25
ndh 2102438 p.Arg202Leu missense_variant 0.18
ndh 2103105 c.-64_-63insG upstream_gene_variant 0.29
katG 2154349 p.Glu588Gly missense_variant 0.22
katG 2155493 p.Asp207His missense_variant 0.12
katG 2155752 c.360C>T synonymous_variant 0.18
katG 2155939 p.Met58Thr missense_variant 0.22
katG 2156007 c.105C>T synonymous_variant 0.12
katG 2156538 c.-427A>G upstream_gene_variant 0.12
PPE35 2167771 p.Ser948Gly missense_variant 0.22
PPE35 2168397 p.Ile739Asn missense_variant 0.17
PPE35 2168409 p.Thr735Ile missense_variant 0.13
PPE35 2168415 p.Gly733Ala missense_variant 0.14
PPE35 2170099 p.Leu172Met missense_variant 0.33
PPE35 2170512 p.Leu34Pro missense_variant 0.2
Rv1979c 2221884 c.1281G>A synonymous_variant 0.18
Rv1979c 2222685 p.Lys160Asn missense_variant 0.29
Rv1979c 2222759 p.Val136Met missense_variant 0.13
Rv1979c 2222765 p.Phe134Leu missense_variant 0.12
Rv1979c 2222862 c.303C>T synonymous_variant 0.17
Rv1979c 2223251 c.-87C>T upstream_gene_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288875 p.Arg123Ser missense_variant 0.14
pncA 2288929 p.Gly105Cys missense_variant 0.12
pncA 2288999 p.Phe81Leu missense_variant 0.17
pncA 2289013 p.Pro77Ser missense_variant 0.14
pncA 2289415 c.-174C>G upstream_gene_variant 0.29
pncA 2289485 c.-244A>G upstream_gene_variant 0.12
kasA 2517927 c.-188G>A upstream_gene_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518280 p.Leu56Ile missense_variant 0.18
kasA 2518781 p.Pro223Ala missense_variant 0.25
kasA 2519320 c.1206C>T synonymous_variant 0.12
kasA 2519348 p.Ala412Ser missense_variant 0.12
eis 2714134 p.Phe400Ser missense_variant 0.12
eis 2714318 p.Arg339Trp missense_variant 0.17
eis 2714457 p.Asp292Glu missense_variant 0.12
eis 2714632 p.Lys234Arg missense_variant 0.13
eis 2714920 p.His138Leu missense_variant 0.33
eis 2715086 p.Ser83Gly missense_variant 0.22
eis 2715231 c.102C>T synonymous_variant 0.22
eis 2715584 c.-252T>C upstream_gene_variant 0.17
ahpC 2726635 p.Ser148Leu missense_variant 0.13
ahpC 2726644 p.Ala151Val missense_variant 0.13
ahpC 2726655 p.Gly155Arg missense_variant 0.12
folC 2747317 c.282C>T synonymous_variant 0.29
folC 2747363 p.Ala79Glu missense_variant 0.22
folC 2747377 c.222C>T synonymous_variant 0.29
folC 2747384 p.Thr72Ser missense_variant 0.33
folC 2747403 p.Ser66Thr missense_variant 0.29
folC 2747656 c.-58G>A upstream_gene_variant 0.17
pepQ 2859409 p.Arg337Leu missense_variant 0.17
pepQ 2860099 p.Leu107Pro missense_variant 0.15
pepQ 2860157 p.Gly88Arg missense_variant 0.25
pepQ 2860469 c.-51C>T upstream_gene_variant 0.13
pepQ 2860613 c.-195C>A upstream_gene_variant 0.22
ribD 2986835 c.-4G>T upstream_gene_variant 0.25
Rv2752c 3066177 c.15T>C synonymous_variant 0.12
Rv2752c 3067072 c.-881C>T upstream_gene_variant 0.25
thyX 3067941 p.Ala2Val missense_variant 0.33
thyA 3074165 p.Ala103Thr missense_variant 0.25
thyA 3074319 p.His51Gln missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448635 c.132C>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474495 c.489A>T synonymous_variant 0.13
fprA 3474838 p.Ile278Phe missense_variant 0.2
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612065 c.1051delG frameshift_variant 0.33
Rv3236c 3612491 p.Leu209Ser missense_variant 0.12
fbiA 3640346 c.-197G>A upstream_gene_variant 0.18
fbiA 3640353 c.-190G>A upstream_gene_variant 0.18
fbiA 3640412 c.-131G>C upstream_gene_variant 0.14
fbiB 3640605 c.-930G>A upstream_gene_variant 0.22
fbiA 3640907 p.Gly122Asp missense_variant 0.2
fbiB 3641031 c.-504C>T upstream_gene_variant 0.14
fbiA 3641050 p.Gln170* stop_gained 0.14
fbiA 3641392 p.Ile284Leu missense_variant 0.18
fbiB 3641762 p.Lys76Asn missense_variant 0.17
fbiB 3641922 p.Ala130Pro missense_variant 0.15
fbiB 3642645 p.Thr371Ser missense_variant 0.14
fbiB 3642813 p.Gly427Arg missense_variant 0.25
alr 3840416 c.1005C>T synonymous_variant 0.2
alr 3840429 p.Asn331Ile missense_variant 0.25
alr 3840436 c.985C>T synonymous_variant 0.25
alr 3840751 p.Glu224* stop_gained 0.29
alr 3841476 c.-56G>C upstream_gene_variant 0.15
rpoA 3877475 p.Glu345Lys missense_variant 0.17
ddn 3987012 p.Gly57Ser missense_variant 0.15
clpC1 4038459 p.Leu749Gln missense_variant 0.14
clpC1 4038616 p.Val697Leu missense_variant 0.14
clpC1 4038724 p.Val661Met missense_variant 0.15
clpC1 4038927 p.Arg593Pro missense_variant 0.18
clpC1 4039345 p.Glu454Lys missense_variant 0.17
clpC1 4039579 p.Asp376Asn missense_variant 0.17
clpC1 4039608 p.Tyr366Phe missense_variant 0.13
clpC1 4040308 c.397C>A synonymous_variant 0.18
clpC1 4040560 p.Leu49Val missense_variant 0.18
embC 4239957 p.Val32Ala missense_variant 0.11
embC 4240872 p.Val337Ala missense_variant 0.13
embC 4240889 p.Trp343Arg missense_variant 0.17
embC 4240955 p.Pro365Thr missense_variant 0.2
embC 4241439 p.Ser526Ile missense_variant 0.18
embC 4241677 c.1815G>A synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243497 p.Val89Leu missense_variant 0.13
embA 4245107 p.Phe625Leu missense_variant 0.12
embA 4245456 p.Glu742Lys missense_variant 0.25
embB 4247740 c.1227G>T synonymous_variant 0.14
embB 4248202 c.1689T>A synonymous_variant 0.14
embB 4248441 p.Thr643Ile missense_variant 0.14
embB 4248474 p.Val654Glu missense_variant 0.29
embB 4249436 p.Gln975* stop_gained 0.13
ubiA 4269602 p.Val78Ile missense_variant 0.22
ethA 4326694 p.Met260Ile missense_variant 0.22
ethR 4326799 c.-750G>A upstream_gene_variant 0.18
ethA 4326906 p.Leu190Phe missense_variant 0.29
ethR 4327574 p.Ala9Val missense_variant 0.18
ethR 4328186 c.639delC frameshift_variant 0.29
whiB6 4338542 c.-21A>G upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408349 c.-147T>C upstream_gene_variant 0.29