Run ID: ERR11465801
Sample name:
Date: 2024-04-15T18:05:41.001423
Number of reads: 836677
Percentage reads mapped: 98.11
Median coverage: 20.0
Strain: lineage4.3.4.1
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.99 |
lineage4.3.4.1 | Euro-American (LAM) | RD174 | 0.99 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.462C>T | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rrs | 1472307 | n.462C>T | non_coding_transcript_exon_variant | 0.23 | streptomycin | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 582 | c.582A>C | synonymous_variant | 0.25 | isoniazid | Not assoc w R - Interim |
gyrA | 6673 | c.-629A>T | upstream_gene_variant | 0.26 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6680 | c.1441C>T | synonymous_variant | 0.25 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7178 | c.-124T>C | upstream_gene_variant | 0.2 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7847 | c.546G>C | synonymous_variant | 0.27 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7853 | c.552C>T | synonymous_variant | 0.28 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7859 | c.558A>C | synonymous_variant | 0.23 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7886 | c.585T>C | synonymous_variant | 0.17 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7892 | c.591G>C | synonymous_variant | 0.21 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7898 | p.Asp199Glu | missense_variant | 0.21 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13483 | p.Ala26Thr | missense_variant | 1.0 | isoniazid | Uncertain significance |
fgd1 | 491610 | c.828A>G | synonymous_variant | 0.17 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491616 | c.834A>G | synonymous_variant | 0.17 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
rpoB | 760181 | c.375T>C | synonymous_variant | 0.26 | rifampicin | Not assoc w R - Interim |
rpoB | 760184 | c.378A>G | synonymous_variant | 0.26 | rifampicin | Not assoc w R - Interim |
rpoB | 761537 | c.1731C>G | synonymous_variant | 0.28 | rifampicin | Not assoc w R - Interim |
rpoB | 761573 | c.1767C>G | synonymous_variant | 0.37 | rifampicin | Not assoc w R - Interim |
rpoB | 761579 | c.1773G>C | synonymous_variant | 0.38 | rifampicin | Not assoc w R - Interim |
rpoB | 761582 | c.1776G>A | synonymous_variant | 0.37 | rifampicin | |
rpoB | 761606 | c.1800C>G | synonymous_variant | 0.4 | rifampicin | |
rpoB | 761612 | c.1806G>T | synonymous_variant | 0.35 | rifampicin | Not assoc w R - Interim |
rpoB | 761615 | c.1809A>C | synonymous_variant | 0.38 | rifampicin | Not assoc w R - Interim |
rpoB | 761636 | c.1830G>T | synonymous_variant | 0.38 | rifampicin | Not assoc w R - Interim |
rpoB | 761645 | c.1839C>G | synonymous_variant | 0.36 | rifampicin | Not assoc w R - Interim |
rpoB | 761648 | c.1842T>C | synonymous_variant | 0.36 | rifampicin | |
rpoC | 763594 | c.225C>T | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
rpoC | 763615 | c.246G>C | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 763618 | c.249C>T | synonymous_variant | 0.2 | rifampicin | |
rpoC | 763624 | c.255C>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 763696 | c.327T>C | synonymous_variant | 0.22 | rifampicin | Not assoc w R - Interim |
rpoC | 763699 | c.330G>C | synonymous_variant | 0.22 | rifampicin | |
rpoC | 763702 | c.333C>G | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
rpoC | 763709 | c.340C>T | synonymous_variant | 0.22 | rifampicin | |
rpoC | 763714 | c.345G>C | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
rpoC | 763717 | c.348T>C | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
rpoC | 763732 | c.363C>G | synonymous_variant | 0.2 | rifampicin | |
rpoC | 763735 | c.366G>C | synonymous_variant | 0.2 | rifampicin | |
rpoC | 764764 | c.1395T>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 764803 | c.1434C>T | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764809 | c.1440C>T | synonymous_variant | 0.18 | rifampicin | Not assoc w R |
rpoC | 764812 | c.1443C>G | synonymous_variant | 0.18 | rifampicin | |
rpoC | 764815 | c.1446A>G | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764824 | c.1455T>C | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 764833 | c.1464A>G | synonymous_variant | 0.2 | rifampicin | |
rpoC | 764836 | c.1467G>A | synonymous_variant | 0.23 | rifampicin | |
rpoC | 764842 | c.1473C>T | synonymous_variant | 0.26 | rifampicin | |
rpoC | 764858 | c.1489T>C | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
rpoC | 764869 | c.1500C>T | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764875 | c.1506C>G | synonymous_variant | 0.18 | rifampicin | |
rpoC | 764893 | c.1524T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 764896 | c.1527C>T | synonymous_variant | 0.14 | rifampicin | |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.86 | rifampicin | Not assoc w R |
rpoC | 765499 | c.2130C>G | synonymous_variant | 0.31 | rifampicin | Not assoc w R - Interim |
rpoC | 765508 | c.2139C>G | synonymous_variant | 0.32 | rifampicin | Not assoc w R - Interim |
rpoC | 766003 | c.2634G>C | synonymous_variant | 0.3 | rifampicin | |
rpoC | 766585 | c.3216T>C | synonymous_variant | 0.21 | rifampicin | |
rpoC | 766607 | c.3238_3240delATCinsCG | frameshift_variant&missense_variant | 0.23 | rifampicin | |
rpoC | 766618 | c.3249G>T | synonymous_variant | 0.24 | rifampicin | |
rpoC | 766624 | c.3255G>C | synonymous_variant | 0.27 | rifampicin | |
rpoC | 766645 | c.3276A>G | synonymous_variant | 0.33 | rifampicin | |
rpoC | 766657 | c.3288A>G | synonymous_variant | 0.33 | rifampicin | |
rpoC | 766667 | p.Ser1100Ala | missense_variant | 0.33 | rifampicin | Uncertain significance |
rpoC | 767059 | c.3690T>G | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
rpoC | 767062 | c.3693C>A | synonymous_variant | 0.24 | rifampicin | |
rpoC | 767098 | c.3729T>C | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
rpoC | 767119 | c.3750A>G | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
rpoC | 767134 | c.3765C>A | synonymous_variant | 0.16 | rifampicin | |
rpoC | 767152 | c.3783T>G | synonymous_variant | 0.19 | rifampicin | |
rpoC | 767155 | c.3786C>G | synonymous_variant | 0.19 | rifampicin | |
rpoC | 767180 | p.Ala1271Gln | missense_variant | 0.16 | rifampicin | |
rpoC | 767191 | c.3822C>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 767206 | c.3837C>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 767302 | c.3933C>G | synonymous_variant | 0.26 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rpsL | 781808 | c.249C>T | synonymous_variant | 0.21 | streptomycin | |
rpsL | 781832 | c.273T>C | synonymous_variant | 0.25 | streptomycin | |
rpsL | 781865 | c.306G>C | synonymous_variant | 0.23 | streptomycin | |
rpsL | 781868 | c.309T>C | synonymous_variant | 0.23 | streptomycin | |
rpsL | 781871 | c.312G>C | synonymous_variant | 0.23 | streptomycin | |
rpsL | 781892 | c.333A>G | synonymous_variant | 0.25 | streptomycin | |
rpsL | 781898 | c.339A>T | synonymous_variant | 0.25 | streptomycin | |
rpsL | 781904 | c.345C>T | synonymous_variant | 0.21 | streptomycin | Not assoc w R - Interim |
rpsL | 781907 | c.348T>C | synonymous_variant | 0.21 | streptomycin | |
rplC | 800747 | c.-62C>G | upstream_gene_variant | 0.17 | linezolid | |
fbiC | 1303536 | c.606G>C | synonymous_variant | 0.23 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fbiC | 1304869 | c.1939C>T | synonymous_variant | 0.23 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
sigE | 1364434 | p.Arg8Trp | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.22 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Uncertain significance | |||||
rrs | 1473290 | n.1445delCinsTT | non_coding_transcript_exon_variant | 0.18 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1473839 | n.182G>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1474266 | n.609T>C | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474291 | n.634_649delTTTCCTCTCCGGAGGAinsC | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
linezolid | ||||||
rrl | 1474308 | n.651G>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474310 | n.653T>G | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1474716 | n.1059A>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475479 | n.1822C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475480 | n.1823A>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475573 | n.1916G>A | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475599 | n.1942A>G | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1475604 | n.1947A>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475606 | n.1949T>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476131 | n.2474C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476299 | n.2642C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1833661 | c.120A>G | synonymous_variant | 0.18 | pyrazinamide | |
rpsA | 1833664 | c.123C>A | synonymous_variant | 0.18 | pyrazinamide | |
rpsA | 1833724 | c.183C>G | synonymous_variant | 0.31 | pyrazinamide | |
rpsA | 1833727 | c.186G>C | synonymous_variant | 0.32 | pyrazinamide | |
rpsA | 1833742 | c.201A>G | synonymous_variant | 0.27 | pyrazinamide | |
rpsA | 1833745 | c.204G>C | synonymous_variant | 0.26 | pyrazinamide | |
rpsA | 1833802 | c.261A>G | synonymous_variant | 0.29 | pyrazinamide | |
rpsA | 1833811 | c.270G>T | synonymous_variant | 0.23 | pyrazinamide | |
rpsA | 1833820 | c.279G>A | synonymous_variant | 0.26 | pyrazinamide | |
rpsA | 1833856 | c.315A>G | synonymous_variant | 0.43 | pyrazinamide | |
rpsA | 1833859 | c.318C>T | synonymous_variant | 0.43 | pyrazinamide | |
rpsA | 1833874 | c.333T>C | synonymous_variant | 0.35 | pyrazinamide | |
rpsA | 1833894 | p.Ala118Glu | missense_variant | 0.31 | pyrazinamide | |
rpsA | 1834030 | c.489C>G | synonymous_variant | 0.35 | pyrazinamide | |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
Rv1979c | 2222854 | p.Ile104Thr | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
mtrB | 3625744 | c.870G>A | synonymous_variant | 0.29 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625747 | c.867G>C | synonymous_variant | 0.27 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625753 | c.859_861delGCCinsAT | frameshift_variant&missense_variant | 0.3 | bedaquiline | Uncertain significance |
rifampicin | Uncertain significance | |||||
mtrB | 3625765 | c.849C>G | synonymous_variant | 0.38 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625774 | c.840G>A | synonymous_variant | 0.41 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625806 | c.808A>C | synonymous_variant | 0.37 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625807 | c.807C>G | synonymous_variant | 0.35 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
lpqB | 3625828 | c.-918G>C | upstream_gene_variant | 0.45 | bedaquiline | |
rifampicin | ||||||
mtrB | 3625852 | c.762A>G | synonymous_variant | 0.47 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625867 | c.747A>G | synonymous_variant | 0.44 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625912 | c.702G>C | synonymous_variant | 0.5 | bedaquiline | |
rifampicin | ||||||
mtrB | 3625915 | c.699G>T | synonymous_variant | 0.5 | bedaquiline | |
rifampicin | ||||||
mtrB | 3627011 | c.-398T>G | upstream_gene_variant | 0.23 | bedaquiline | |
rifampicin | ||||||
rpoA | 3877613 | p.Ile299Val | missense_variant | 0.48 | rifampicin | |
rpoA | 3877656 | c.852T>C | synonymous_variant | 0.29 | rifampicin | Not assoc w R - Interim |
rpoA | 3877665 | c.843C>A | synonymous_variant | 0.31 | rifampicin | |
rpoA | 3877668 | c.840A>G | synonymous_variant | 0.29 | rifampicin | |
rpoA | 3877677 | c.829_831delGCGinsTC | frameshift_variant&missense_variant | 0.36 | rifampicin | |
rpoA | 3877680 | c.828G>C | synonymous_variant | 0.36 | rifampicin | Not assoc w R - Interim |
rpoA | 3877686 | c.822A>G | synonymous_variant | 0.36 | rifampicin | Not assoc w R - Interim |
rpoA | 3877692 | c.816G>C | synonymous_variant | 0.44 | rifampicin | Not assoc w R - Interim |
rpoA | 3877704 | c.804G>C | synonymous_variant | 0.44 | rifampicin | |
rpoA | 3878364 | c.144A>C | synonymous_variant | 0.21 | rifampicin | |
rpoA | 3878370 | c.138T>C | synonymous_variant | 0.19 | rifampicin | |
rpoA | 3878385 | c.123C>G | synonymous_variant | 0.19 | rifampicin | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.89 | pyrazinamide | Not assoc w R |
clpC1 | 4038725 | c.1980C>G | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4039991 | c.714G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
panD | 4044090 | c.192C>A | synonymous_variant | 0.35 | pyrazinamide | |
glpK | 4138574 | c.1182G>C | synonymous_variant | 0.25 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
embC | 4240795 | c.933C>G | synonymous_variant | 0.15 | ethambutol | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245077 | c.1845G>C | synonymous_variant | 0.21 | ethambutol | |
embA | 4245083 | c.1851A>G | synonymous_variant | 0.18 | ethambutol | Not assoc w R - Interim |
embA | 4245113 | c.1881C>A | synonymous_variant | 0.15 | ethambutol | |
embA | 4245137 | c.1905T>C | synonymous_variant | 0.16 | ethambutol | |
embB | 4247512 | c.999T>C | synonymous_variant | 0.23 | ethambutol | |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |