TB-Profiler result

Run: ERR11465801
Summary

Run ID: ERR11465801

Sample name:

Date: 03-01-2024 09:24:24

Number of reads: 836677

Percentage reads mapped: 98.11

Strain: lineage4.3.4.1

Drug-resistance: Other

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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 R rrs n.462C>T (0.23)
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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.23 streptomycin
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 6673 c.-629A>T upstream_gene_variant 0.26
gyrA 6680 c.-622C>T upstream_gene_variant 0.25
gyrA 7178 c.-124T>C upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7847 c.546G>C synonymous_variant 0.27
gyrA 7853 c.552C>T synonymous_variant 0.28
gyrA 7859 c.558A>C synonymous_variant 0.23
gyrA 7886 c.585T>C synonymous_variant 0.17
gyrA 7892 c.591G>C synonymous_variant 0.21
gyrA 7898 p.Asp199Glu missense_variant 0.21
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491610 c.828A>G synonymous_variant 0.17
fgd1 491616 c.834A>G synonymous_variant 0.17
rpoB 760181 c.375T>C synonymous_variant 0.26
rpoB 760184 c.378A>G synonymous_variant 0.26
rpoB 761537 c.1731C>G synonymous_variant 0.28
rpoB 761573 c.1767C>G synonymous_variant 0.37
rpoB 761579 c.1773G>C synonymous_variant 0.38
rpoB 761582 c.1776G>A synonymous_variant 0.37
rpoB 761606 c.1800C>G synonymous_variant 0.4
rpoB 761612 c.1806G>T synonymous_variant 0.35
rpoB 761615 c.1809A>C synonymous_variant 0.38
rpoB 761636 c.1830G>T synonymous_variant 0.38
rpoB 761645 c.1839C>G synonymous_variant 0.36
rpoB 761648 c.1842T>C synonymous_variant 0.36
rpoC 763594 c.225C>T synonymous_variant 0.24
rpoC 763615 c.246G>C synonymous_variant 0.2
rpoC 763618 c.249C>T synonymous_variant 0.2
rpoC 763624 c.255C>G synonymous_variant 0.17
rpoC 763696 c.327T>C synonymous_variant 0.22
rpoC 763699 c.330G>C synonymous_variant 0.22
rpoC 763702 c.333C>G synonymous_variant 0.21
rpoC 763709 c.340C>T synonymous_variant 0.22
rpoC 763714 c.345G>C synonymous_variant 0.23
rpoC 763717 c.348T>C synonymous_variant 0.24
rpoC 763732 c.363C>G synonymous_variant 0.2
rpoC 763735 c.366G>C synonymous_variant 0.2
rpoC 764764 c.1395T>C synonymous_variant 0.16
rpoC 764803 c.1434C>T synonymous_variant 0.18
rpoC 764809 c.1440C>T synonymous_variant 0.18
rpoC 764812 c.1443C>G synonymous_variant 0.18
rpoC 764815 c.1446A>G synonymous_variant 0.18
rpoC 764824 c.1455T>C synonymous_variant 0.2
rpoC 764833 c.1464A>G synonymous_variant 0.2
rpoC 764836 c.1467G>A synonymous_variant 0.23
rpoC 764842 c.1473C>T synonymous_variant 0.26
rpoC 764858 c.1489T>C synonymous_variant 0.21
rpoC 764869 c.1500C>T synonymous_variant 0.18
rpoC 764875 c.1506C>G synonymous_variant 0.18
rpoC 764893 c.1524T>C synonymous_variant 0.15
rpoC 764896 c.1527C>T synonymous_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.86
rpoC 765499 c.2130C>G synonymous_variant 0.31
rpoC 765508 c.2139C>G synonymous_variant 0.32
rpoC 766003 c.2634G>C synonymous_variant 0.3
rpoC 766585 c.3216T>C synonymous_variant 0.21
rpoC 766607 p.Ile1080Leu missense_variant 0.23
rpoC 766618 c.3249G>T synonymous_variant 0.24
rpoC 766624 c.3255G>C synonymous_variant 0.27
rpoC 766645 c.3276A>G synonymous_variant 0.33
rpoC 766657 c.3288A>G synonymous_variant 0.33
rpoC 766667 p.Ser1100Ala missense_variant 0.33
rpoC 767059 c.3690T>G synonymous_variant 0.24
rpoC 767062 c.3693C>A synonymous_variant 0.24
rpoC 767098 c.3729T>C synonymous_variant 0.21
rpoC 767119 c.3750A>G synonymous_variant 0.21
rpoC 767134 c.3765C>A synonymous_variant 0.16
rpoC 767152 c.3783T>G synonymous_variant 0.19
rpoC 767155 c.3786C>G synonymous_variant 0.19
rpoC 767180 p.Ala1271Gln missense_variant 0.16
rpoC 767191 c.3822C>G synonymous_variant 0.15
rpoC 767206 c.3837C>G synonymous_variant 0.15
rpoC 767302 c.3933C>G synonymous_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781808 c.249C>T synonymous_variant 0.21
rpsL 781832 c.273T>C synonymous_variant 0.25
rpsL 781865 c.306G>C synonymous_variant 0.23
rpsL 781868 c.309T>C synonymous_variant 0.23
rpsL 781871 c.312G>C synonymous_variant 0.23
rpsL 781892 c.333A>G synonymous_variant 0.25
rpsL 781898 c.339A>T synonymous_variant 0.25
rpsL 781904 c.345C>T synonymous_variant 0.21
rpsL 781907 c.348T>C synonymous_variant 0.21
rplC 800747 c.-62C>G upstream_gene_variant 0.17
fbiC 1303536 c.606G>C synonymous_variant 0.23
fbiC 1304869 c.1939C>T synonymous_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.22
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.18
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.2
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.27
rrl 1474291 n.634_649delTTTCCTCTCCGGAGGAinsC non_coding_transcript_exon_variant 0.18
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.16
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.16
rrl 1474716 n.1059A>C non_coding_transcript_exon_variant 0.22
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.18
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.29
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.29
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.3
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.29
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.35
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.29
rrl 1475604 n.1947A>C non_coding_transcript_exon_variant 0.25
rrl 1475606 n.1949T>C non_coding_transcript_exon_variant 0.25
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.17
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.22
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.23
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.29
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.3
rpsA 1833661 c.120A>G synonymous_variant 0.18
rpsA 1833664 c.123C>A synonymous_variant 0.18
rpsA 1833724 c.183C>G synonymous_variant 0.31
rpsA 1833727 c.186G>C synonymous_variant 0.32
rpsA 1833742 c.201A>G synonymous_variant 0.27
rpsA 1833745 c.204G>C synonymous_variant 0.26
rpsA 1833802 c.261A>G synonymous_variant 0.29
rpsA 1833811 c.270G>T synonymous_variant 0.23
rpsA 1833820 c.279G>A synonymous_variant 0.26
rpsA 1833856 c.315A>G synonymous_variant 0.43
rpsA 1833859 c.318C>T synonymous_variant 0.43
rpsA 1833874 c.333T>C synonymous_variant 0.35
rpsA 1833894 p.Ala118Glu missense_variant 0.31
rpsA 1834030 c.489C>G synonymous_variant 0.35
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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 3877613 p.Ile299Val missense_variant 0.48
rpoA 3877656 c.852T>C synonymous_variant 0.29
rpoA 3877665 c.843C>A synonymous_variant 0.31
rpoA 3877668 c.840A>G synonymous_variant 0.29
rpoA 3877677 p.Ala277Ser missense_variant 0.36
rpoA 3877680 c.828G>C synonymous_variant 0.36
rpoA 3877686 c.822A>G synonymous_variant 0.36
rpoA 3877692 c.816G>C synonymous_variant 0.44
rpoA 3877704 c.804G>C synonymous_variant 0.44
rpoA 3878364 c.144A>C synonymous_variant 0.21
rpoA 3878370 c.138T>C synonymous_variant 0.19
rpoA 3878385 c.123C>G synonymous_variant 0.19
clpC1 4038287 c.2418C>T synonymous_variant 0.89
clpC1 4038725 c.1980C>G synonymous_variant 0.15
clpC1 4039991 c.714G>A synonymous_variant 1.0
panD 4044090 c.192C>A synonymous_variant 0.35
embC 4240795 c.933C>G synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245077 c.1845G>C synonymous_variant 0.21
embA 4245083 c.1851A>G synonymous_variant 0.18
embA 4245113 c.1881C>A synonymous_variant 0.15
embA 4245137 c.1905T>C synonymous_variant 0.16
embB 4247512 c.999T>C synonymous_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0