TB-Profiler result

Run: ERR1213932
Summary

Run ID: ERR1213932

Sample name:

Date: 31-03-2023 12:44:53

Number of reads: 1226174

Percentage reads mapped: 89.02

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 Euro-American T;X;H None 0.97
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.97
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 7031 p.Gly598Arg missense_variant 0.12
gyrA 7225 c.-77T>C upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7460 c.159C>A synonymous_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7728 c.427A>C synonymous_variant 0.11
gyrA 7742 c.441G>A synonymous_variant 0.12
gyrA 7763 c.462T>G synonymous_variant 0.14
gyrA 7793 c.492G>C synonymous_variant 0.2
gyrA 7799 c.498A>G synonymous_variant 0.14
gyrA 7802 c.501C>G synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760235 c.429T>C synonymous_variant 0.18
rpoB 760244 c.438G>C synonymous_variant 0.18
rpoB 760283 c.477G>C synonymous_variant 0.13
rpoB 762239 c.2433G>A synonymous_variant 0.25
rpoC 763492 c.123G>C synonymous_variant 0.11
rpoC 763528 c.159G>A synonymous_variant 0.12
rpoC 763546 c.177A>G synonymous_variant 0.13
rpoC 763723 c.354G>C synonymous_variant 0.11
rpoC 763741 c.372C>T synonymous_variant 0.12
rpoC 763747 c.378G>A synonymous_variant 0.12
rpoC 763765 c.396T>G synonymous_variant 0.13
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.14
rpoC 764431 c.1062G>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.13
rpoC 764435 c.1066_1068delAGGinsCGA synonymous_variant 0.13
rpoC 764446 c.1077T>C synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766459 c.3090G>C synonymous_variant 0.2
rpoC 766480 c.3111C>T synonymous_variant 0.2
rpoC 766483 c.3114G>T synonymous_variant 0.19
rpoC 766484 p.Val1039Ile missense_variant 0.19
rpoC 766492 c.3123T>G synonymous_variant 0.23
rpoC 766493 p.Gly1042Asn missense_variant 0.23
rpoC 766504 c.3135G>C synonymous_variant 0.2
rpoC 766517 p.Thr1050Ala missense_variant 0.18
rpoC 766528 c.3159T>C synonymous_variant 0.13
rpoC 766534 c.3165C>G synonymous_variant 0.13
rpoC 766738 c.3369G>T synonymous_variant 0.13
rpoC 766741 c.3372G>C synonymous_variant 0.12
rpoC 766765 c.3396A>C synonymous_variant 0.2
rpoC 766771 c.3402G>C synonymous_variant 0.12
rpoC 766774 c.3405T>C synonymous_variant 0.17
rpoC 766777 c.3408C>G synonymous_variant 0.11
rpoC 766798 c.3429C>G synonymous_variant 0.13
rpoC 766804 c.3435A>G synonymous_variant 0.27
rpoC 766807 c.3438T>C synonymous_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776081 c.2400G>C synonymous_variant 0.14
mmpL5 776084 c.2397C>G synonymous_variant 0.14
mmpL5 776087 c.2394C>G synonymous_variant 0.14
mmpL5 776093 c.2388C>A synonymous_variant 0.15
mmpL5 776099 p.Thr794Leu missense_variant 0.15
mmpL5 776107 c.2374C>T synonymous_variant 0.12
mmpL5 777613 p.Gly290Arg missense_variant 0.18
mmpS5 778655 p.Ala84Val missense_variant 0.93
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781929 p.Gly124Ser missense_variant 0.11
fbiC 1304580 c.1650T>C synonymous_variant 0.17
fbiC 1304613 c.1683T>C synonymous_variant 0.12
fbiC 1304640 c.1710A>C synonymous_variant 0.11
fbiC 1304727 c.1797A>C synonymous_variant 0.11
fbiC 1304991 c.2061G>C synonymous_variant 0.15
fbiC 1304994 c.2064A>G synonymous_variant 0.15
fbiC 1304995 p.Leu689Glu missense_variant 0.15
fbiC 1305004 p.Glu692Asn missense_variant 0.18
fbiC 1305007 p.Ile693Val missense_variant 0.2
fbiC 1305012 c.2082G>C synonymous_variant 0.18
fbiC 1305015 c.2085G>A synonymous_variant 0.18
fbiC 1305033 c.2103T>G synonymous_variant 0.18
fbiC 1305381 c.2451G>C synonymous_variant 0.29
fbiC 1305393 c.2463T>C synonymous_variant 0.22
fbiC 1305396 c.2466C>G synonymous_variant 0.22
fbiC 1305400 p.His824Asn missense_variant 0.2
fbiC 1305405 c.2475A>C synonymous_variant 0.2
fbiC 1305408 c.2478G>A synonymous_variant 0.2
fbiC 1305420 c.2490C>G synonymous_variant 0.2
fbiC 1305423 c.2493T>A synonymous_variant 0.2
fbiC 1305426 c.2496G>A synonymous_variant 0.2
fbiC 1305429 c.2499G>C synonymous_variant 0.18
fbiC 1305462 c.2532G>C synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.22
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.6
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.25
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.21
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.24
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.14
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.17
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.15
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.33
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.36
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.38
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.45
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.44
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.18
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.22
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.21
rrl 1475479 n.1822C>G non_coding_transcript_exon_variant 0.21
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.25
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.2
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.14
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.46
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.43
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.43
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.43
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.43
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.43
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.12
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.12
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.14
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.15
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.13
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.11
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.15
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.2
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.2
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.23
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.21
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.21
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.23
rrl 1476679 n.3022T>C non_coding_transcript_exon_variant 0.25
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.17
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.17
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.17
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.17
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.17
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.13
inhA 1674846 p.Ile215Met missense_variant 0.18
inhA 1674852 c.651G>C synonymous_variant 0.2
inhA 1674858 c.657G>A synonymous_variant 0.22
inhA 1674879 c.678T>G synonymous_variant 0.22
inhA 1674904 p.Ala235Pro missense_variant 0.29
rpsA 1834097 c.556_557delTCinsAG synonymous_variant 0.12
rpsA 1834102 c.561T>C synonymous_variant 0.13
rpsA 1834123 c.582C>T synonymous_variant 0.12
rpsA 1834189 c.648G>C synonymous_variant 0.18
rpsA 1834213 c.672G>C synonymous_variant 0.13
rpsA 1834225 c.684C>T synonymous_variant 0.15
rpsA 1834234 c.693G>C synonymous_variant 0.15
rpsA 1834240 c.699T>C synonymous_variant 0.17
rpsA 1834249 c.708T>C synonymous_variant 0.22
rpsA 1834261 c.720A>G synonymous_variant 0.14
rpsA 1834264 c.723G>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.4
PPE35 2170187 p.Glu142Asp missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517941 c.-174C>G upstream_gene_variant 0.13
kasA 2517959 c.-156C>T upstream_gene_variant 0.13
kasA 2517962 c.-153C>G upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715467 c.-135A>C upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.2
folC 2747196 p.Asp135Asn missense_variant 0.14
ribD 2986991 c.153C>T synonymous_variant 0.13
thyA 3073806 c.666C>G synonymous_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612455 p.Arg221Leu missense_variant 0.25
rpoA 3877587 c.921A>G synonymous_variant 0.14
rpoA 3877590 c.918G>C synonymous_variant 0.14
rpoA 3877593 c.915C>T synonymous_variant 0.14
rpoA 3877638 c.870T>C synonymous_variant 0.11
clpC1 4039085 c.1620A>G synonymous_variant 0.2
clpC1 4039610 c.1095G>C synonymous_variant 0.12
clpC1 4039613 c.1092C>T synonymous_variant 0.12
clpC1 4039622 c.1083C>T synonymous_variant 0.13
clpC1 4039649 c.1056G>C synonymous_variant 0.11
clpC1 4039652 c.1053G>C synonymous_variant 0.11
clpC1 4039670 c.1035G>C synonymous_variant 0.1
clpC1 4039682 c.1023C>G synonymous_variant 0.14
clpC1 4039694 c.1011G>C synonymous_variant 0.15
embC 4239680 c.-183C>T upstream_gene_variant 0.2
embC 4241298 p.Ala479Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244092 p.Ala287Asp missense_variant 0.18
embA 4246265 p.His1011Gln missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0