TB-Profiler result

Run: SRR4035745
Summary

Run ID: SRR4035745

Sample name:

Date: 04-04-2023 07:16:23

Number of reads: 1071633

Percentage reads mapped: 99.42

Strain: lineage4.1.2

Drug-resistance: Other

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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 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
ethA 4326841 p.Tyr211* stop_gained 0.12 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 5102 c.-138T>G upstream_gene_variant 0.22
gyrB 5599 c.360G>A synonymous_variant 0.13
gyrB 5631 p.Leu131Pro missense_variant 0.12
gyrB 5647 p.Glu136Asp missense_variant 0.14
gyrB 6157 p.Asn306Lys missense_variant 0.18
gyrB 6173 p.Glu312Lys missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7452 p.Val51Leu missense_variant 0.12
gyrA 7461 c.163delG frameshift_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490697 c.-86C>T upstream_gene_variant 0.12
fgd1 490714 c.-69G>C upstream_gene_variant 0.11
fgd1 491344 p.Ala188Ser missense_variant 0.22
fgd1 491357 p.Phe192Ser missense_variant 0.2
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575391 p.Gln15Leu missense_variant 0.25
mshA 575926 c.579A>G synonymous_variant 0.13
mshA 576093 p.Pro249Gln missense_variant 0.13
mshA 576107 p.Ala254Thr missense_variant 0.13
ccsA 619994 p.Glu35Ala missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761062 p.Ala419Asp missense_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764672 p.Gln435Glu missense_variant 0.11
rpoC 764790 p.Arg474His missense_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765382 c.2013G>A synonymous_variant 0.15
rpoC 765394 c.2025G>A synonymous_variant 0.15
rpoC 766632 p.Val1088Glu missense_variant 0.15
rpoC 766721 p.Pro1118Ala missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776463 p.Ser673Leu missense_variant 0.15
mmpL5 777035 p.Gln482His missense_variant 0.12
mmpL5 777309 p.Gly391Asp missense_variant 0.17
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777328 p.Ala385Thr missense_variant 0.18
mmpL5 777878 p.Asp201Glu missense_variant 0.12
mmpL5 778972 c.-492G>A upstream_gene_variant 0.12
mmpL5 779313 c.-833G>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800874 p.Arg22Ser missense_variant 0.18
rplC 800884 p.Val26Met missense_variant 0.14
rplC 800895 c.87C>T synonymous_variant 0.14
fbiC 1303350 c.420C>T synonymous_variant 0.13
fbiC 1304032 p.Glu368Lys missense_variant 0.18
fbiC 1304233 p.Trp435Arg missense_variant 0.2
Rv1258c 1406657 c.684C>T synonymous_variant 0.13
Rv1258c 1406869 p.Pro158Ser missense_variant 0.13
Rv1258c 1407481 c.-141G>C upstream_gene_variant 0.12
embR 1416540 p.Ala270Thr missense_variant 0.2
embR 1417084 p.Ile88Met missense_variant 0.18
atpE 1460876 c.-169G>A upstream_gene_variant 0.15
atpE 1461262 p.Leu73Gln missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.11
rrl 1475015 n.1358C>T non_coding_transcript_exon_variant 0.13
rrl 1475749 n.2093delA non_coding_transcript_exon_variant 0.11
fabG1 1673306 c.-134A>T upstream_gene_variant 0.13
fabG1 1673328 c.-112A>G upstream_gene_variant 0.15
inhA 1674697 p.Ser166Gly missense_variant 0.12
rpsA 1834635 p.Ala365Gly missense_variant 0.15
tlyA 1917814 c.-126C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102052 p.Gly331Cys missense_variant 0.13
ndh 2102053 c.990G>A synonymous_variant 0.13
katG 2153913 p.Asn733Lys missense_variant 0.2
katG 2153976 c.2136C>T synonymous_variant 0.2
katG 2154384 c.1728G>A synonymous_variant 0.15
katG 2155352 p.Arg254Cys missense_variant 0.14
katG 2155458 c.654C>T synonymous_variant 0.15
PPE35 2169102 p.Pro504Arg missense_variant 0.14
PPE35 2169192 c.1420delG frameshift_variant 0.18
PPE35 2169550 p.Gly355Arg missense_variant 0.12
PPE35 2169624 p.Gly330Val missense_variant 0.12
PPE35 2169674 p.Asn313Lys missense_variant 0.14
PPE35 2170314 p.Val100Ala missense_variant 0.12
PPE35 2170324 p.Phe97Leu missense_variant 0.13
Rv1979c 2222105 p.Ala354Pro missense_variant 0.12
Rv1979c 2222625 c.540C>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289394 c.-153A>G upstream_gene_variant 0.14
pncA 2289667 c.-426C>T upstream_gene_variant 0.18
pncA 2289956 c.-715C>G upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519327 p.Gly405Cys missense_variant 0.13
kasA 2519337 p.Asn408Ile missense_variant 0.14
eis 2714955 c.378C>T synonymous_variant 0.15
ahpC 2725926 c.-267T>C upstream_gene_variant 0.15
pepQ 2859314 c.1105C>T synonymous_variant 0.14
pepQ 2859381 c.1038C>A synonymous_variant 0.13
ribD 2986708 c.-131G>A upstream_gene_variant 0.15
ribD 2987216 c.378T>A synonymous_variant 0.15
Rv2752c 3067157 c.-966G>A upstream_gene_variant 0.12
thyA 3074137 p.Ile112Asn missense_variant 0.2
thyA 3074619 c.-148C>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338929 c.-189A>T upstream_gene_variant 0.2
fbiD 3339285 c.168G>A synonymous_variant 0.13
Rv3083 3449237 p.Arg245Met missense_variant 0.12
fprA 3473971 c.-36T>A upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474063 c.57G>A synonymous_variant 0.17
fprA 3474705 c.699T>A synonymous_variant 0.18
fprA 3475002 c.996G>T synonymous_variant 0.33
whiB7 3568444 p.His79Leu missense_variant 0.15
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612995 p.Leu41Ser missense_variant 0.13
Rv3236c 3613003 c.114G>A synonymous_variant 0.17
Rv3236c 3613256 c.-140T>A upstream_gene_variant 0.2
fbiB 3642243 p.Ala237Thr missense_variant 0.25
fbiB 3642400 p.Pro289Leu missense_variant 0.15
fbiB 3642546 p.Gly338Ser missense_variant 0.2
fbiB 3642559 p.Tyr342Phe missense_variant 0.17
fbiB 3642668 c.1134A>G synonymous_variant 0.12
alr 3840482 c.939T>G synonymous_variant 0.12
alr 3840528 p.Thr298Ile missense_variant 0.2
alr 3840798 p.Asn208Ile missense_variant 0.12
alr 3841179 p.Ala81Gly missense_variant 0.14
clpC1 4038918 p.Gly596Val missense_variant 0.12
clpC1 4038980 c.1725C>T synonymous_variant 0.15
clpC1 4039513 p.Lys398Gln missense_variant 0.14
clpC1 4039710 p.Ile332Asn missense_variant 0.22
clpC1 4039956 p.Leu250Pro missense_variant 0.13
embC 4240673 p.Gly271Ser missense_variant 0.29
embC 4241138 p.Ala426Thr missense_variant 0.13
embC 4241470 c.1608C>G synonymous_variant 0.2
embC 4242176 p.Pro772Ser missense_variant 0.25
embC 4242469 p.Tyr869* stop_gained 0.17
embC 4242527 p.Gly889Arg missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242890 p.Arg1010Trp missense_variant 0.14
embA 4243614 p.Arg128Cys missense_variant 0.13
embA 4244065 p.Leu278Gln missense_variant 0.2
embA 4244074 p.Ala281Val missense_variant 0.22
embA 4244102 c.870A>G synonymous_variant 0.17
embA 4244330 c.1098G>T synonymous_variant 0.12
embA 4244957 c.1725C>G synonymous_variant 0.11
embB 4248167 p.Thr552Ala missense_variant 0.15
embB 4248190 c.1677G>T synonymous_variant 0.15
embB 4248226 c.1713G>A synonymous_variant 0.14
embB 4248317 p.Val602Ile missense_variant 0.19
aftB 4267252 p.Asp529Asn missense_variant 0.14
aftB 4267700 p.Trp379Cys missense_variant 0.17
aftB 4267904 c.933G>A synonymous_variant 0.18
ubiA 4269269 p.Ala189Pro missense_variant 0.12
ethA 4326846 p.Thr210Ala missense_variant 0.13
ethA 4326855 p.Arg207Cys missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408338 c.-136A>G upstream_gene_variant 0.11