TB-Profiler result

Run: ERR4814658
Summary

Run ID: ERR4814658

Sample name:

Date: 01-04-2023 13:25:09

Number of reads: 817475

Percentage reads mapped: 99.57

Strain: lineage4.1.2.1

Drug-resistance: Sensitive

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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 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.99
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
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 7121 p.Pro628Thr missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7440 p.Gly47Arg missense_variant 0.33
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7617 p.Arg106Cys missense_variant 0.33
gyrA 8169 p.Gln290* stop_gained 0.14
gyrA 8190 p.Ala297Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575335 c.-13G>T upstream_gene_variant 0.14
mshA 575562 p.Met72Thr missense_variant 0.12
mshA 575654 p.Val103Leu missense_variant 0.17
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575883 p.Thr179Met missense_variant 0.15
mshA 576489 p.Val381Glu missense_variant 0.2
ccsA 620084 p.Ala65Glu missense_variant 0.18
ccsA 620376 c.486G>T synonymous_variant 0.22
ccsA 620426 p.Val179Ala missense_variant 0.11
rpoB 759632 c.-175A>T upstream_gene_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761330 c.1524G>C synonymous_variant 0.2
rpoB 761819 c.2013G>A synonymous_variant 0.12
rpoC 763527 p.Gly53Glu missense_variant 0.17
rpoC 763591 c.222C>A synonymous_variant 0.14
rpoC 763851 p.Ala161Val missense_variant 0.15
rpoC 764541 p.Val391Gly missense_variant 0.1
rpoC 764543 p.Thr392Ala missense_variant 0.1
rpoC 764596 c.1227G>A synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765507 p.Val713Ala missense_variant 0.1
rpoC 765557 p.Thr730Ser missense_variant 0.17
rpoC 767266 c.3897G>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776955 p.Lys509Ile missense_variant 0.18
mmpL5 777157 c.1324C>A synonymous_variant 0.14
mmpL5 777164 c.1317C>T synonymous_variant 0.23
mmpL5 777173 c.1308C>T synonymous_variant 0.13
mmpL5 777176 p.Glu435Asp missense_variant 0.13
mmpL5 777196 p.Glu429Gln missense_variant 0.1
mmpL5 777596 c.885G>A synonymous_variant 0.15
mmpL5 777782 c.699G>A synonymous_variant 0.5
mmpL5 779031 c.-551G>T upstream_gene_variant 0.12
mmpR5 779109 p.Leu40Phe missense_variant 0.2
mmpL5 779361 c.-881C>T upstream_gene_variant 0.25
mmpR5 779378 p.Pro130Arg missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781420 c.-140C>A upstream_gene_variant 0.12
rpsL 781800 p.Leu81Met missense_variant 0.11
fbiC 1302995 p.Asn22Ile missense_variant 0.17
fbiC 1304409 c.1479C>A synonymous_variant 0.18
fbiC 1304466 c.1536C>A synonymous_variant 0.15
Rv1258c 1407226 p.Gly39Ser missense_variant 0.18
embR 1417012 c.336G>A synonymous_variant 0.15
atpE 1460855 c.-189delC upstream_gene_variant 0.12
atpE 1461063 p.Ala7Ser missense_variant 0.15
atpE 1461071 c.27C>T synonymous_variant 0.17
atpE 1461137 c.93C>T synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473515 n.-143G>A upstream_gene_variant 0.2
fabG1 1673810 p.Ser124Leu missense_variant 0.12
fabG1 1674010 p.Thr191Ala missense_variant 0.12
tlyA 1917805 c.-135C>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918319 p.Arg127Gln missense_variant 0.15
tlyA 1918576 c.637C>A synonymous_variant 0.17
ndh 2102517 p.Val176Ile missense_variant 0.18
katG 2154551 p.Leu521Met missense_variant 0.12
katG 2155207 p.Ser302Ile missense_variant 0.11
katG 2155345 p.Ala256Asp missense_variant 0.29
katG 2155464 c.648G>T synonymous_variant 0.11
Rv1979c 2222421 c.744G>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518143 p.Gly10Asp missense_variant 0.25
kasA 2519153 p.Ile347Val missense_variant 0.4
kasA 2519317 c.1203G>A synonymous_variant 0.14
ahpC 2725938 c.-255G>T upstream_gene_variant 0.11
folC 2747167 p.Lys144Asn missense_variant 0.12
folC 2747434 p.Asp55Glu missense_variant 0.12
folC 2747452 c.136_146dupAGCCTGACCCG frameshift_variant&stop_gained 0.22
pepQ 2859641 p.Gly260Ser missense_variant 0.5
pepQ 2859807 c.612C>T synonymous_variant 1.0
pepQ 2860074 p.Glu115Asp missense_variant 0.12
ribD 2986993 p.Gly52Val missense_variant 0.14
ribD 2987116 p.Tyr93Cys missense_variant 0.11
Rv2752c 3065668 p.Gln175Arg missense_variant 0.11
thyX 3067627 c.318delG frameshift_variant 0.11
thyX 3067631 c.315C>A synonymous_variant 0.11
thyX 3067926 p.Leu7Pro missense_variant 0.17
thyA 3074047 p.Ala142Val missense_variant 1.0
thyA 3074128 p.Ala115Glu missense_variant 0.2
thyA 3074342 p.Leu44Met missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339265 p.Ala50Thr missense_variant 0.12
Rv3083 3448354 c.-150C>A upstream_gene_variant 0.2
Rv3083 3448388 c.-116C>A upstream_gene_variant 0.14
Rv3083 3448567 p.His22Tyr missense_variant 0.12
Rv3083 3448652 p.Tyr50Cys missense_variant 0.4
Rv3083 3449016 c.513A>G synonymous_variant 0.11
Rv3083 3449202 p.Phe233Leu missense_variant 0.12
Rv3083 3449684 p.Ser394Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474092 p.Thr29Asn missense_variant 0.13
fprA 3474158 p.Ser51Phe missense_variant 0.13
fprA 3474715 p.Asp237Asn missense_variant 0.14
whiB7 3568712 c.-33C>G upstream_gene_variant 1.0
Rv3236c 3611994 p.Gly375Ser missense_variant 0.22
Rv3236c 3612810 p.Pro103Ser missense_variant 0.15
fbiA 3640705 p.Gly55Arg missense_variant 0.14
fbiA 3641480 p.Pro313Leu missense_variant 0.12
fbiB 3641637 p.Ala35Ser missense_variant 0.11
fbiB 3641973 p.Val147Phe missense_variant 0.25
fbiB 3642639 p.Glu369* stop_gained 0.14
alr 3840457 c.964C>T synonymous_variant 0.12
alr 3840607 p.Val272Leu missense_variant 0.15
alr 3840645 p.Gly259Val missense_variant 0.12
rpoA 3878631 c.-124C>T upstream_gene_variant 1.0
clpC1 4038236 c.2469C>G synonymous_variant 0.18
clpC1 4038262 p.Asp815Tyr missense_variant 0.2
clpC1 4040343 p.Ala121Asp missense_variant 0.12
clpC1 4040411 c.294T>G synonymous_variant 0.12
clpC1 4040415 p.Gln97Arg missense_variant 0.12
clpC1 4040417 c.288G>T synonymous_variant 0.12
clpC1 4040487 p.Ala73Glu missense_variant 0.12
panD 4044110 p.Tyr58His missense_variant 0.1
panD 4044141 c.141C>T synonymous_variant 0.11
panD 4044248 p.Arg12Cys missense_variant 0.33
embC 4240658 p.Arg266Ser missense_variant 0.2
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244698 p.Val489Asp missense_variant 0.13
embA 4244934 p.Thr568Ala missense_variant 0.12
embA 4245365 p.Phe711Leu missense_variant 0.22
embB 4245566 c.-948C>T upstream_gene_variant 0.14
embB 4245653 c.-861C>T upstream_gene_variant 0.4
embB 4246859 p.Val116Ile missense_variant 0.14
embB 4247428 c.915C>A synonymous_variant 0.12
embB 4247537 p.His342Asn missense_variant 0.13
embB 4247791 p.Ser426Arg missense_variant 0.17
embB 4249773 p.Gly1087Asp missense_variant 0.14
aftB 4267398 p.Pro480Leu missense_variant 0.12
aftB 4267426 p.Gly471Arg missense_variant 0.18
aftB 4267986 p.Arg284Leu missense_variant 0.17
ubiA 4269605 p.Asp77Tyr missense_variant 0.12
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.15
ethR 4326970 c.-579G>T upstream_gene_variant 0.27
ethR 4326982 c.-567C>G upstream_gene_variant 0.18
ethA 4327686 c.-213C>T upstream_gene_variant 0.13
whiB6 4338361 p.Arg54Gln missense_variant 0.15
whiB6 4338571 c.-50G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407615 p.Leu196Phe missense_variant 0.11
gid 4408190 p.Glu5Lys missense_variant 0.13
gid 4408307 c.-105G>T upstream_gene_variant 0.25