TB-Profiler result

Run: ERR2517489

Summary

Run ID: ERR2517489

Sample name:

Date: 20-10-2023 00:06:42

Number of reads: 4877619

Percentage reads mapped: 90.82

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
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
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.98
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.498A>G synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491542 c.760T>C synonymous_variant 0.16
fgd1 491547 c.765A>C synonymous_variant 0.16
fgd1 491550 c.768T>C synonymous_variant 0.16
fgd1 491591 p.Lys270Met missense_variant 0.92
mshA 575679 p.Asn111Ser missense_variant 0.94
rpoB 760115 c.309C>T synonymous_variant 0.99
rpoB 760430 c.624T>C synonymous_variant 0.15
rpoB 760522 p.Ser239Asn missense_variant 0.16
rpoB 760532 c.726T>C synonymous_variant 0.15
rpoB 760533 p.Val243Thr missense_variant 0.14
rpoB 760547 c.741G>C synonymous_variant 0.16
rpoB 760563 p.Arg253Met missense_variant 0.14
rpoB 760591 p.Val262Ala missense_variant 0.15
rpoB 760611 c.805T>C synonymous_variant 0.16
rpoB 760634 c.828T>C synonymous_variant 0.16
rpoB 760646 c.840C>G synonymous_variant 0.17
rpoB 760655 c.849A>G synonymous_variant 0.15
rpoB 760661 c.855A>C synonymous_variant 0.15
rpoB 760670 c.864G>C synonymous_variant 0.14
rpoB 760683 c.877T>C synonymous_variant 0.14
rpoB 760970 c.1164G>C synonymous_variant 0.16
rpoB 760982 c.1176G>C synonymous_variant 0.16
rpoB 760985 c.1179G>C synonymous_variant 0.15
rpoB 761015 c.1209G>C synonymous_variant 0.13
rpoC 763076 c.-294C>G upstream_gene_variant 0.14
rpoC 763085 c.-285C>G upstream_gene_variant 0.14
rpoC 763744 c.375G>C synonymous_variant 0.14
rpoC 764530 c.1161C>G synonymous_variant 0.13
rpoC 764893 c.1524T>C synonymous_variant 0.14
rpoC 764911 c.1542A>G synonymous_variant 0.15
rpoC 764923 c.1554A>G synonymous_variant 0.15
rpoC 764932 c.1563C>A synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 0.99
rpoC 765556 c.2187G>C synonymous_variant 0.14
rpoC 765559 c.2190G>C synonymous_variant 0.14
rpoC 765578 c.2209C>T synonymous_variant 0.15
rpoC 765583 c.2214G>T synonymous_variant 0.15
rpoC 766630 c.3261G>C synonymous_variant 0.15
rpoC 766894 c.3525T>C synonymous_variant 0.14
rpoC 766895 c.3526T>C synonymous_variant 0.14
rpoC 766972 c.3603G>C synonymous_variant 0.16
rpoC 766978 c.3609C>G synonymous_variant 0.16
rpoC 767033 p.Ser1222Thr missense_variant 0.16
rpoC 767059 c.3690T>G synonymous_variant 0.18
rpoC 767062 c.3693C>A synonymous_variant 0.19
rpoC 767074 c.3705T>C synonymous_variant 0.21
rpoC 767098 c.3729T>C synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303920 c.990C>G synonymous_variant 0.14
fbiC 1303923 c.993C>T synonymous_variant 0.14
fbiC 1303929 c.999G>C synonymous_variant 0.15
fbiC 1304817 c.1887T>C synonymous_variant 0.14
fbiC 1304853 c.1923C>G synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.2
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.2
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.2
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.21
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.2
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.17
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.18
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.18
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.15
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.15
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.15
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.19
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.17
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.15
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.19
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.18
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.21
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.15
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.18
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.17
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.18
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.18
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.18
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.18
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.17
rrl 1475271 n.1614A>C non_coding_transcript_exon_variant 0.16
rrl 1475273 n.1616T>A non_coding_transcript_exon_variant 0.15
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.16
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.16
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.16
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.17
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.17
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.17
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.19
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.16
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.15
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.15
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.16
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14
rpsA 1833838 c.297G>C synonymous_variant 0.14
rpsA 1833847 c.306C>G synonymous_variant 0.15
rpsA 1833856 c.315A>G synonymous_variant 0.15
rpsA 1833862 c.321G>T synonymous_variant 0.15
rpsA 1833874 c.333T>C synonymous_variant 0.15
rpsA 1834240 c.699T>C synonymous_variant 0.13
rpsA 1834249 c.708T>C synonymous_variant 0.14
rpsA 1834261 c.720A>C synonymous_variant 0.14
rpsA 1834306 c.765T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154907 p.Glu402Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517947 c.-168C>T upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518816 c.702C>A synonymous_variant 0.13
thyA 3073977 c.495A>G synonymous_variant 0.16
thyA 3074001 c.471C>G synonymous_variant 0.14
thyA 3074004 c.468T>C synonymous_variant 0.14
thyA 3074037 c.435C>G synonymous_variant 0.13
ald 3086767 c.-53A>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878391 c.117T>C synonymous_variant 0.14
rpoA 3878396 c.112C>T synonymous_variant 0.15
rpoA 3878436 c.72A>G synonymous_variant 0.15
rpoA 3878442 c.66G>C synonymous_variant 0.14
rpoA 3878454 c.54A>C synonymous_variant 0.14
rpoA 3878472 p.Asp12Glu missense_variant 0.14
clpC1 4038755 c.1950G>C synonymous_variant 0.14
clpC1 4038773 c.1932T>C synonymous_variant 0.15
clpC1 4038782 c.1923G>C synonymous_variant 0.15
clpC1 4038790 c.1915C>T synonymous_variant 0.15
clpC1 4038812 c.1893T>C synonymous_variant 0.14
clpC1 4038878 c.1827A>G synonymous_variant 0.14
clpC1 4038953 c.1752A>G synonymous_variant 0.14
clpC1 4039682 c.1023C>G synonymous_variant 0.15
clpC1 4039685 c.1020C>T synonymous_variant 0.14
embC 4241137 c.1275G>C synonymous_variant 0.16
embC 4241140 c.1278A>G synonymous_variant 0.16
embC 4241141 p.Ile427Val missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248070 c.1557T>C synonymous_variant 0.13
ubiA 4269919 c.-86T>G upstream_gene_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0