TB-Profiler result

Run: ERR11465151
Summary

Run ID: ERR11465151

Sample name:

Date: 06-01-2024 14:31:43

Number of reads: 1435501

Percentage reads mapped: 99.11

Strain: lineage4.3.4.1

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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
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
gyrA 6634 c.-668T>C upstream_gene_variant 0.14
gyrA 6640 c.-662A>C upstream_gene_variant 0.14
gyrA 6643 c.-659A>G upstream_gene_variant 0.14
gyrA 6655 c.-647T>C upstream_gene_variant 0.14
gyrA 6745 c.-557T>C upstream_gene_variant 0.15
gyrA 6775 c.-527G>C upstream_gene_variant 0.16
gyrA 6781 c.-521C>T upstream_gene_variant 0.16
gyrA 6793 c.-509T>C upstream_gene_variant 0.12
gyrB 6798 p.Gly520Ala missense_variant 0.16
gyrA 6824 c.-478C>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8250 p.Glu317Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760118 c.312T>C synonymous_variant 0.12
rpoB 760121 c.315T>C synonymous_variant 0.12
rpoB 760184 c.378A>G synonymous_variant 0.12
rpoB 760196 c.390C>G synonymous_variant 0.14
rpoB 761954 c.2148C>G synonymous_variant 0.15
rpoB 761999 c.2193G>C synonymous_variant 0.12
rpoB 762008 c.2202C>T synonymous_variant 0.16
rpoB 762038 c.2232C>T synonymous_variant 0.15
rpoC 763127 c.-243G>C upstream_gene_variant 0.18
rpoC 763142 c.-228C>G upstream_gene_variant 0.13
rpoC 763259 c.-111G>C upstream_gene_variant 0.12
rpoC 763268 c.-102C>G upstream_gene_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.16
rpoC 763675 c.306C>G synonymous_variant 0.16
rpoC 763732 c.363C>G synonymous_variant 0.13
rpoC 763741 c.372C>T synonymous_variant 0.14
rpoC 763744 c.375G>C synonymous_variant 0.13
rpoC 764239 c.870T>C synonymous_variant 0.32
rpoC 764245 c.876C>T synonymous_variant 0.3
rpoC 764431 c.1062G>C synonymous_variant 0.18
rpoC 764434 c.1065A>G synonymous_variant 0.18
rpoC 764746 c.1377G>T synonymous_variant 0.17
rpoC 764791 c.1422C>G synonymous_variant 0.15
rpoC 764797 c.1428G>C synonymous_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.93
rpoC 765826 c.2457T>C synonymous_variant 0.2
rpoC 766504 c.3135G>C synonymous_variant 0.23
rpoC 766517 p.Thr1050Ala missense_variant 0.25
rpoC 766522 c.3153C>A synonymous_variant 0.25
rpoC 766525 c.3156G>C synonymous_variant 0.23
rpoC 766528 c.3159T>G synonymous_variant 0.23
rpoC 766530 p.Arg1054Gln missense_variant 0.22
rpoC 766537 c.3168G>A synonymous_variant 0.22
rpoC 766540 p.Asp1057Glu missense_variant 0.22
rpoC 766546 p.Glu1059Asp missense_variant 0.22
rpoC 766549 c.3180G>C synonymous_variant 0.21
rpoC 766843 c.3474T>C synonymous_variant 0.19
rpoC 766846 c.3477C>G synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800633 c.-176T>C upstream_gene_variant 0.15
rplC 800654 c.-155T>C upstream_gene_variant 0.18
rplC 800759 c.-50C>T upstream_gene_variant 0.15
rplC 800762 c.-47T>G upstream_gene_variant 0.14
fbiC 1304817 c.1887T>C synonymous_variant 0.18
fbiC 1304826 c.1896G>C synonymous_variant 0.18
fbiC 1304829 c.1899T>C synonymous_variant 0.19
fbiC 1304832 c.1902C>G synonymous_variant 0.19
fbiC 1304853 c.1923C>T synonymous_variant 0.18
fbiC 1304856 c.1926C>G synonymous_variant 0.17
fbiC 1304869 c.1939C>T synonymous_variant 0.17
fbiC 1304874 c.1944C>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.29
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.19
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.22
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.23
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.55
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.28
rrl 1473717 n.60G>A non_coding_transcript_exon_variant 0.16
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.17
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.4
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.23
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.24
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.26
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.38
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.22
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.22
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.22
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.25
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.23
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.26
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.26
rrl 1475707 n.2050T>G non_coding_transcript_exon_variant 0.23
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.33
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.31
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.3
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.13
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.17
rpsA 1833829 c.288A>G synonymous_variant 0.31
rpsA 1833832 c.291G>A synonymous_variant 0.34
rpsA 1833838 c.297G>C synonymous_variant 0.24
rpsA 1833841 c.300C>G synonymous_variant 0.24
rpsA 1833847 c.306C>G synonymous_variant 0.28
rpsA 1833856 c.315A>G synonymous_variant 0.24
rpsA 1833862 c.321G>T synonymous_variant 0.19
rpsA 1833892 c.351G>A synonymous_variant 0.19
rpsA 1833894 p.Ala118Glu missense_variant 0.19
rpsA 1833949 c.408T>C synonymous_variant 0.19
rpsA 1834303 c.762T>G synonymous_variant 0.23
rpsA 1834306 c.765T>C synonymous_variant 0.23
rpsA 1834690 c.1149T>C synonymous_variant 0.26
rpsA 1834732 c.1191T>C synonymous_variant 0.35
rpsA 1834733 p.Ala398Pro missense_variant 0.31
rpsA 1834738 c.1197A>G synonymous_variant 0.33
rpsA 1834747 c.1206A>G synonymous_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3877593 c.915C>T synonymous_variant 0.14
rpoA 3877602 c.906C>T synonymous_variant 0.16
rpoA 3877608 c.900G>A synonymous_variant 0.16
rpoA 3877656 c.852T>G synonymous_variant 0.16
rpoA 3877848 c.660C>T synonymous_variant 0.14
rpoA 3877857 c.651G>A synonymous_variant 0.17
rpoA 3877926 c.582G>C synonymous_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 0.97
clpC1 4039226 c.1479T>C synonymous_variant 0.16
clpC1 4039241 c.1464G>C synonymous_variant 0.21
clpC1 4039517 c.1188C>G synonymous_variant 0.2
clpC1 4039576 p.Ala377Ser missense_variant 0.19
clpC1 4039991 c.714G>A synonymous_variant 1.0
clpC1 4040411 c.294T>C synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0