TB-Profiler result

Run: ERR11465152
Summary

Run ID: ERR11465152

Sample name:

Date: 06-01-2024 14:37:15

Number of reads: 2022043

Percentage reads mapped: 99.14

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 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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 6242 p.Arg335Lys missense_variant 0.15
gyrB 6250 c.1011A>G synonymous_variant 0.14
gyrB 6253 c.1014G>C synonymous_variant 0.13
gyrB 6292 c.1053G>C synonymous_variant 0.13
gyrA 6634 c.-668T>C upstream_gene_variant 0.15
gyrA 6640 c.-662A>C upstream_gene_variant 0.15
gyrA 6643 c.-659A>G upstream_gene_variant 0.16
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7394 c.93T>C synonymous_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8250 p.Glu317Gln missense_variant 0.99
gyrA 8829 c.1528T>C synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575824 c.477T>A synonymous_variant 0.16
rpoB 760101 c.295T>C synonymous_variant 0.17
rpoB 760430 c.624T>C synonymous_variant 0.17
rpoB 760611 c.805_807delTTGinsCTC synonymous_variant 0.16
rpoB 760670 c.864G>C synonymous_variant 0.14
rpoB 760674 c.868T>C synonymous_variant 0.13
rpoB 760679 c.873A>G synonymous_variant 0.13
rpoB 761948 c.2142G>C synonymous_variant 0.15
rpoB 761954 c.2148C>G synonymous_variant 0.14
rpoB 761999 c.2193G>C synonymous_variant 0.18
rpoB 762008 c.2202C>T synonymous_variant 0.14
rpoB 762038 c.2232C>T synonymous_variant 0.18
rpoB 762101 c.2295C>G synonymous_variant 0.16
rpoB 762114 p.Ile770Val missense_variant 0.13
rpoC 763127 c.-243G>C upstream_gene_variant 0.13
rpoC 763139 c.-231C>T upstream_gene_variant 0.14
rpoC 763142 c.-228C>G upstream_gene_variant 0.15
rpoC 763546 c.177A>G synonymous_variant 0.15
rpoC 763570 c.201G>C synonymous_variant 0.17
rpoC 763573 c.204G>C synonymous_variant 0.17
rpoC 763765 c.396T>C synonymous_variant 0.15
rpoC 763774 c.405G>C synonymous_variant 0.14
rpoC 763781 p.Ser138Ala missense_variant 0.15
rpoC 763807 c.438T>C synonymous_variant 0.13
rpoC 763813 c.444C>G synonymous_variant 0.16
rpoC 764153 p.Gln262Lys missense_variant 0.21
rpoC 764431 c.1062G>C synonymous_variant 0.19
rpoC 764434 c.1065A>G synonymous_variant 0.2
rpoC 764449 c.1080G>C synonymous_variant 0.17
rpoC 764452 c.1083T>C synonymous_variant 0.17
rpoC 764458 c.1089G>C synonymous_variant 0.19
rpoC 764461 c.1092A>G synonymous_variant 0.18
rpoC 764485 c.1116G>C synonymous_variant 0.19
rpoC 764491 c.1122G>T synonymous_variant 0.2
rpoC 764497 c.1128A>G synonymous_variant 0.19
rpoC 764500 c.1131C>G synonymous_variant 0.13
rpoC 764521 c.1152T>C synonymous_variant 0.23
rpoC 764527 c.1158C>T synonymous_variant 0.17
rpoC 764530 c.1161C>T synonymous_variant 0.15
rpoC 764536 c.1167G>T synonymous_variant 0.23
rpoC 764539 c.1170C>G synonymous_variant 0.24
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765425 p.Lys686Glu missense_variant 0.12
rpoC 765478 c.2109T>C synonymous_variant 0.14
rpoC 765499 c.2130C>G synonymous_variant 0.14
rpoC 766738 c.3369G>T synonymous_variant 0.16
rpoC 766765 c.3396A>C synonymous_variant 0.14
rpoC 766771 c.3402G>C synonymous_variant 0.12
rpoC 766774 c.3405T>C synonymous_variant 0.13
rpoC 766777 c.3408C>G synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776695 p.Val596Ile missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781793 c.234G>C synonymous_variant 0.14
rplC 800654 c.-155T>C upstream_gene_variant 0.15
fbiC 1304715 c.1785G>T synonymous_variant 0.16
fbiC 1304724 c.1794A>G synonymous_variant 0.24
fbiC 1304727 c.1797A>G synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.32
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.15
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.21
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.44
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.19
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.22
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.18
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.22
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.32
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.28
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.19
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.23
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.29
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.2
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.17
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.21
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.25
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.19
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.19
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.19
rrl 1475707 n.2050T>G non_coding_transcript_exon_variant 0.3
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.27
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.21
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.36
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.19
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.12
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.19
inhA 1674690 c.489C>G synonymous_variant 0.15
inhA 1674858 c.657G>A synonymous_variant 0.17
rpsA 1833694 c.153G>C synonymous_variant 0.16
rpsA 1833697 c.156C>G synonymous_variant 0.14
rpsA 1833847 c.306C>G synonymous_variant 0.2
rpsA 1834456 c.915T>G synonymous_variant 0.17
rpsA 1834639 c.1098T>C synonymous_variant 0.17
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
kasA 2517941 c.-174C>G upstream_gene_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
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 3877740 c.768G>C synonymous_variant 0.13
rpoA 3877776 c.732T>C synonymous_variant 0.15
rpoA 3877848 c.660C>T synonymous_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038755 c.1950G>T synonymous_variant 0.17
clpC1 4038767 c.1938G>C synonymous_variant 0.13
clpC1 4038773 c.1932T>C synonymous_variant 0.12
clpC1 4038790 c.1915C>T synonymous_variant 0.14
clpC1 4038812 c.1893T>C synonymous_variant 0.2
clpC1 4038839 c.1866G>C synonymous_variant 0.13
clpC1 4038842 c.1863G>C synonymous_variant 0.14
clpC1 4038878 c.1827A>G synonymous_variant 0.15
clpC1 4038905 c.1800A>C synonymous_variant 0.16
clpC1 4038908 c.1797C>G synonymous_variant 0.18
clpC1 4038911 c.1794G>T synonymous_variant 0.18
clpC1 4038914 c.1791G>C synonymous_variant 0.18
clpC1 4038917 c.1788C>T synonymous_variant 0.16
clpC1 4038923 c.1782A>G synonymous_variant 0.18
clpC1 4038932 c.1773G>C synonymous_variant 0.18
clpC1 4038953 c.1752A>G synonymous_variant 0.17
clpC1 4038965 c.1740T>C synonymous_variant 0.24
clpC1 4038971 c.1734T>C synonymous_variant 0.17
clpC1 4039121 c.1584T>C synonymous_variant 0.17
clpC1 4039124 c.1581C>G synonymous_variant 0.16
clpC1 4039220 c.1485G>C synonymous_variant 0.15
clpC1 4039517 c.1188C>G synonymous_variant 0.13
clpC1 4039991 c.714G>A synonymous_variant 1.0
clpC1 4040393 c.312G>C synonymous_variant 0.12
clpC1 4040423 c.282A>G synonymous_variant 0.13
clpC1 4040444 c.261C>G synonymous_variant 0.13
clpC1 4040450 c.255A>G synonymous_variant 0.15
clpC1 4040537 c.168G>C synonymous_variant 0.13
clpC1 4040644 c.61A>C synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0