TB-Profiler result

Run: ERR5908227
Summary

Run ID: ERR5908227

Sample name:

Date: 02-04-2023 00:54:09

Number of reads: 459884

Percentage reads mapped: 99.44

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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 2155499 c.612delG frameshift_variant 0.15 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 5050 c.-190G>T upstream_gene_variant 0.17
gyrB 5125 c.-115G>T upstream_gene_variant 0.18
gyrB 6996 p.Glu586Gly missense_variant 0.2
gyrA 7033 c.-269G>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8191 p.Ala297Gly missense_variant 0.2
gyrA 8239 p.Arg313His missense_variant 0.17
gyrA 8320 p.Ser340Ile missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9439 p.Ser713* stop_gained 0.17
fgd1 490965 c.183C>A synonymous_variant 0.22
fgd1 490982 p.Arg67Gln missense_variant 0.22
fgd1 491444 p.Ser221Tyr missense_variant 0.2
mshA 575587 c.240C>A synonymous_variant 0.13
mshA 575801 p.His152Asn missense_variant 0.14
mshA 575842 c.495G>A synonymous_variant 0.17
mshA 575965 c.618C>T synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.43
ccsA 619842 c.-49G>T upstream_gene_variant 0.22
ccsA 619889 c.-2G>T upstream_gene_variant 0.15
ccsA 620730 p.His280Gln missense_variant 0.15
rpoB 761571 p.Pro589Ser missense_variant 0.5
rpoC 762743 c.-627G>A upstream_gene_variant 0.25
rpoC 762860 c.-510G>A upstream_gene_variant 0.12
rpoC 763568 c.199C>A synonymous_variant 0.4
rpoC 763790 p.Glu141* stop_gained 0.15
rpoC 763963 c.594C>G synonymous_variant 0.4
rpoC 764369 c.1000C>A synonymous_variant 0.22
rpoC 765196 c.1827T>A synonymous_variant 0.15
rpoC 765386 p.Phe673Ile missense_variant 0.15
rpoC 765433 p.Met688Ile missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775716 p.Arg922Gln missense_variant 0.17
mmpL5 775793 c.2688C>T synonymous_variant 0.18
mmpL5 776421 p.Asp687Val missense_variant 0.29
mmpL5 777596 c.885G>T synonymous_variant 0.2
mmpL5 778478 c.3G>T start_lost 0.14
mmpL5 778687 c.-207C>T upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781554 c.-6C>T upstream_gene_variant 0.14
rplC 801144 c.336C>T synonymous_variant 0.2
rplC 801193 p.Arg129Trp missense_variant 0.15
fbiC 1303564 p.Gly212Ser missense_variant 0.12
fbiC 1303664 p.Leu245Arg missense_variant 0.22
fbiC 1304369 p.Val480Ala missense_variant 0.2
Rv1258c 1406355 p.Gln329Pro missense_variant 0.2
Rv1258c 1406873 c.468C>T synonymous_variant 0.14
Rv1258c 1407049 p.Gly98Ser missense_variant 0.5
embR 1416398 p.Asp317Val missense_variant 0.14
atpE 1461112 p.Gly23Asp missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472855 n.1010A>C non_coding_transcript_exon_variant 1.0
inhA 1673340 c.-862G>A upstream_gene_variant 0.15
fabG1 1673835 p.Phe132Leu missense_variant 0.14
inhA 1674976 p.Tyr259His missense_variant 0.15
rpsA 1833545 p.Pro2Ser missense_variant 0.17
rpsA 1833737 p.Arg66Cys missense_variant 0.25
rpsA 1834168 c.627C>A synonymous_variant 0.17
rpsA 1834364 p.Ser275Pro missense_variant 0.17
rpsA 1834507 c.966C>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918199 p.Leu87Gln missense_variant 0.22
tlyA 1918258 p.His107Asn missense_variant 0.11
tlyA 1918302 c.363G>A synonymous_variant 0.12
tlyA 1918320 c.381G>A synonymous_variant 0.14
ndh 2102257 c.786C>T synonymous_variant 0.14
ndh 2102406 p.Leu213Met missense_variant 0.15
ndh 2103236 c.-194C>A upstream_gene_variant 0.17
ndh 2103239 c.-197T>C upstream_gene_variant 0.17
katG 2154185 c.1927C>T synonymous_variant 0.14
katG 2154186 c.1926G>C synonymous_variant 0.14
PPE35 2168331 p.Leu761Pro missense_variant 0.2
PPE35 2168380 p.Thr745Ala missense_variant 0.33
PPE35 2168631 p.Asn661Ser missense_variant 0.14
PPE35 2168730 p.Pro628Leu missense_variant 0.25
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2169894 p.Gly240Ala missense_variant 0.15
Rv1979c 2222074 p.Pro364Gln missense_variant 0.18
Rv1979c 2223278 c.-114G>A upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289059 c.183A>T synonymous_variant 0.18
pncA 2289439 c.-198C>T upstream_gene_variant 0.17
pncA 2289456 c.-215G>T upstream_gene_variant 0.2
pncA 2289735 c.-494C>A upstream_gene_variant 0.12
pncA 2290202 c.-961C>T upstream_gene_variant 0.17
pncA 2290240 c.-999A>G upstream_gene_variant 0.2
kasA 2518904 p.Arg264Gly missense_variant 0.25
eis 2714455 p.Gly293Asp missense_variant 0.12
folC 2747353 c.246C>A synonymous_variant 0.18
Rv2752c 3065402 c.790C>A synonymous_variant 0.18
Rv2752c 3066111 c.81C>A synonymous_variant 0.18
thyX 3067885 p.Pro21Ser missense_variant 0.29
thyX 3067924 p.Arg8Ser missense_variant 0.25
thyX 3068009 c.-64G>T upstream_gene_variant 0.12
thyA 3073894 p.Gly193Val missense_variant 0.33
thyA 3074275 p.Asp66Gly missense_variant 0.11
thyA 3074466 c.6G>T synonymous_variant 0.11
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086818 c.-2T>A upstream_gene_variant 0.5
Rv3083 3448541 p.Gly13Val missense_variant 0.12
Rv3083 3448782 c.279C>A synonymous_variant 0.2
Rv3083 3449592 c.1089C>T synonymous_variant 0.18
Rv3083 3449722 p.Cys407Ser missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474239 p.Phe78Ser missense_variant 0.2
fprA 3474465 c.459C>T synonymous_variant 0.14
fprA 3474606 c.600A>T synonymous_variant 0.15
fprA 3474686 p.Pro227Gln missense_variant 0.2
fprA 3474982 p.Gly326Arg missense_variant 0.15
Rv3236c 3612178 c.939C>A synonymous_variant 0.29
Rv3236c 3612507 p.His204Tyr missense_variant 0.17
Rv3236c 3612596 p.Thr174Ile missense_variant 0.29
fbiB 3641109 c.-426C>A upstream_gene_variant 0.14
fbiA 3641219 p.Val226Ala missense_variant 0.18
fbiA 3641453 p.Arg304Leu missense_variant 0.11
fbiB 3641564 c.30G>T synonymous_variant 0.12
fbiB 3641966 c.432C>T synonymous_variant 0.5
fbiB 3642609 p.Ser359Arg missense_variant 0.11
alr 3840212 c.1209C>A synonymous_variant 0.15
rpoA 3877600 p.Gln303Arg missense_variant 0.17
rpoA 3878002 p.Ser169Leu missense_variant 0.12
rpoA 3878519 c.-12A>G upstream_gene_variant 0.33
ddn 3986679 c.-165A>T upstream_gene_variant 0.2
ddn 3987140 p.Gln99His missense_variant 0.17
ddn 3987213 p.Pro124Ser missense_variant 0.18
clpC1 4038327 p.Glu793Gly missense_variant 0.25
clpC1 4038377 c.2328C>A synonymous_variant 0.18
clpC1 4039988 c.717C>A synonymous_variant 0.15
clpC1 4040585 p.Glu40Asp missense_variant 0.22
clpC1 4040874 c.-170C>T upstream_gene_variant 0.33
embC 4240015 c.153G>T synonymous_variant 0.12
embC 4240753 c.891C>A synonymous_variant 0.2
embC 4241008 c.1146G>T synonymous_variant 0.14
embC 4241622 p.Thr587Asn missense_variant 0.33
embC 4241644 c.1782G>A synonymous_variant 1.0
embC 4242049 c.2187C>G synonymous_variant 0.25
embC 4242254 p.Pro798Thr missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242931 c.-302G>A upstream_gene_variant 0.14
embA 4244823 p.Val531Met missense_variant 0.14
embA 4246159 p.Pro976Gln missense_variant 0.2
embB 4246310 c.-204C>T upstream_gene_variant 1.0
embB 4246940 p.Pro143Thr missense_variant 0.22
embB 4248848 p.Pro779Ser missense_variant 0.18
embB 4248986 p.Gly825Arg missense_variant 0.18
embB 4249118 p.Asp869Tyr missense_variant 0.22
embB 4249285 c.2773delC frameshift_variant 0.14
embB 4249594 c.3081G>A synonymous_variant 1.0
aftB 4268097 p.Gly247Val missense_variant 0.22
aftB 4268456 c.381G>A synonymous_variant 0.25
ethA 4326701 p.Arg258Pro missense_variant 0.13
ethA 4326754 p.Trp240Cys missense_variant 0.15
ethR 4327607 p.Pro20Gln missense_variant 0.2
ethR 4327780 p.Arg78Trp missense_variant 0.17
ethR 4327796 p.Ala83Asp missense_variant 0.17
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407581 p.Gly208Arg missense_variant 0.11
gid 4407800 p.Val135Leu missense_variant 0.13
gid 4407930 c.273A>G synonymous_variant 0.12
gid 4408093 p.Gly37Val missense_variant 0.14
gid 4408455 c.-253T>C upstream_gene_variant 0.12