TB-Profiler result

Run: ERR9634265
Summary

Run ID: ERR9634265

Sample name:

Date: 2024-03-26T12:59:56.719977

Number of reads: 220869

Percentage reads mapped: 68.97

Median coverage: 5.0

Strain: lineage4.3.4.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.5
lineage4.3.4 Euro-American (LAM) RD174 0.31
lineage4.3.4.2 Euro-American (LAM) RD174 0.87
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
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 Drugs Confidence
gyrA 7523 c.222C>G synonymous_variant 0.5 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7526 c.225G>C synonymous_variant 0.5 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7532 c.231T>C synonymous_variant 0.53 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 0.5 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 0.5 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7559 c.258G>C synonymous_variant 0.47 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7622 c.321C>T synonymous_variant 0.67 levofloxacin
moxifloxacin
gyrA 7631 c.330G>C synonymous_variant 0.71 levofloxacin
moxifloxacin
gyrA 7637 c.336C>T synonymous_variant 0.68 levofloxacin
moxifloxacin
gyrA 7652 c.351C>T synonymous_variant 0.67 levofloxacin
moxifloxacin
gyrA 7658 c.357A>G synonymous_variant 0.59 levofloxacin
moxifloxacin
gyrA 7661 c.360C>T synonymous_variant 0.59 levofloxacin
moxifloxacin
gyrA 7664 c.363T>C synonymous_variant 0.62 levofloxacin
moxifloxacin
gyrA 7667 c.366C>T synonymous_variant 0.62 levofloxacin
moxifloxacin
gyrA 7670 c.369A>G synonymous_variant 0.62 levofloxacin
moxifloxacin
gyrA 7676 c.375G>C synonymous_variant 0.62 levofloxacin
moxifloxacin
gyrA 7679 c.378G>C synonymous_variant 0.62 levofloxacin
moxifloxacin
gyrA 7683 c.382_384delAGGinsCT frameshift_variant&missense_variant 0.62 levofloxacin
moxifloxacin
gyrA 7694 c.393A>G synonymous_variant 0.61 levofloxacin
moxifloxacin
gyrA 7697 c.396C>G synonymous_variant 0.61 levofloxacin
moxifloxacin
gyrA 7706 c.405C>T synonymous_variant 0.61 levofloxacin
moxifloxacin
gyrA 7709 c.408G>C synonymous_variant 0.61 levofloxacin
moxifloxacin
gyrA 7710 c.409T>C synonymous_variant 0.61 levofloxacin
moxifloxacin
gyrA 7728 c.427_429delAGGinsCT frameshift_variant&missense_variant 0.65 levofloxacin
moxifloxacin
gyrA 7760 c.459C>T synonymous_variant 0.61 levofloxacin
moxifloxacin
gyrA 7763 c.462T>G synonymous_variant 0.61 levofloxacin
moxifloxacin
gyrA 7784 c.483A>G synonymous_variant 0.46 levofloxacin
moxifloxacin
ccsA 620604 c.714C>G synonymous_variant 0.58 capreomycin
amikacin
kanamycin
ccsA 620605 c.715_717delGTTinsAC frameshift_variant&missense_variant 0.58 capreomycin
amikacin
kanamycin
ccsA 620619 c.729G>C synonymous_variant 0.58 capreomycin
amikacin
kanamycin
ccsA 620622 c.732G>C synonymous_variant 0.58 capreomycin
amikacin
kanamycin
ccsA 620625 c.735A>C synonymous_variant 0.58 capreomycin
amikacin
kanamycin
ccsA 620649 c.759A>G synonymous_variant 0.71 capreomycin
amikacin
kanamycin
ccsA 620658 c.768C>T synonymous_variant 0.67 capreomycin
amikacin
kanamycin
ccsA 620676 c.786C>T synonymous_variant 0.7 capreomycin
amikacin
kanamycin
ccsA 620694 c.804C>G synonymous_variant 0.75 capreomycin
amikacin
kanamycin
ccsA 620698 p.Val270Ile missense_variant 0.75 capreomycin
amikacin
kanamycin
ccsA 620730 c.840C>T synonymous_variant 0.62 capreomycin
amikacin
kanamycin
ccsA 620733 c.843G>C synonymous_variant 0.64 capreomycin
amikacin
kanamycin
ccsA 620736 c.846G>C synonymous_variant 0.62 capreomycin
amikacin
kanamycin
ccsA 620739 c.849A>G synonymous_variant 0.62 capreomycin
amikacin
kanamycin
ccsA 620742 c.852G>C synonymous_variant 0.62 capreomycin
amikacin
kanamycin
ccsA 620748 c.858T>C synonymous_variant 0.65 capreomycin
amikacin
kanamycin
ccsA 620766 c.876C>A synonymous_variant 0.65 capreomycin
amikacin
kanamycin
ccsA 620778 c.888T>C synonymous_variant 0.64 capreomycin
amikacin
kanamycin
ccsA 620783 p.Ala298Val missense_variant 0.67 capreomycin
amikacin
kanamycin
ccsA 620793 c.903G>C synonymous_variant 0.59 capreomycin
amikacin
kanamycin
ccsA 620796 c.906C>G synonymous_variant 0.6 capreomycin
amikacin
kanamycin
ccsA 620802 c.912C>G synonymous_variant 0.57 capreomycin
amikacin
kanamycin
ccsA 620808 c.918T>C synonymous_variant 0.54 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620809 c.919C>T synonymous_variant 0.54 capreomycin
amikacin
kanamycin
ccsA 620818 c.928_930delGTTinsAC frameshift_variant&missense_variant 0.55 capreomycin
amikacin
kanamycin
nusG 734421 c.168A>C synonymous_variant 0.62 rifampicin
nusG 734424 c.171G>C synonymous_variant 0.64 rifampicin
nusG 734439 c.186C>G synonymous_variant 0.71 rifampicin
nusG 734442 c.189G>A synonymous_variant 0.71 rifampicin
nusG 734451 c.198G>C synonymous_variant 0.75 rifampicin
nusG 734454 c.201A>G synonymous_variant 0.75 rifampicin
nusG 734460 c.207G>C synonymous_variant 0.75 rifampicin
nusG 734472 c.219T>G synonymous_variant 0.8 rifampicin Not assoc w R - Interim
nusG 734475 c.222T>C synonymous_variant 0.8 rifampicin Not assoc w R - Interim
nusG 734499 c.246G>C synonymous_variant 0.86 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.91 rifampicin Not assoc w R - Interim
rpoB 760181 c.375T>C synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoC 765496 c.2127C>G synonymous_variant 0.5 rifampicin
rpoC 765499 c.2130C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 765533 p.Tyr722His missense_variant 0.46 rifampicin Uncertain significance
mmpL5 775856 c.2625T>C synonymous_variant 0.71 clofazimine
bedaquiline
mmpL5 775862 c.2619G>C synonymous_variant 0.62 clofazimine
bedaquiline
mmpL5 775865 c.2616T>C synonymous_variant 0.62 clofazimine
bedaquiline
mmpL5 775886 c.2595A>C synonymous_variant 0.67 clofazimine
bedaquiline
mmpL5 775904 c.2577G>A synonymous_variant 0.78 clofazimine
bedaquiline
mmpL5 775910 c.2571G>A synonymous_variant 0.82 clofazimine
bedaquiline
mmpL5 775916 c.2565T>C synonymous_variant 0.73 clofazimine
bedaquiline
mmpL5 775922 c.2559G>C synonymous_variant 0.5 clofazimine
bedaquiline
mmpL5 775951 c.2530C>T synonymous_variant 0.67 clofazimine
bedaquiline
mmpL5 775961 c.2520C>G synonymous_variant 0.86 clofazimine
bedaquiline
mmpL5 775966 p.Ala839Ser missense_variant 0.65 clofazimine
bedaquiline
mmpL5 775970 c.2511G>C synonymous_variant 0.7 clofazimine
bedaquiline
mmpL5 775975 c.2506T>C synonymous_variant 0.82 clofazimine
bedaquiline
mmpL5 775981 p.Leu834Met missense_variant 0.82 clofazimine
bedaquiline
mmpL5 775991 c.2490G>A synonymous_variant 0.79 clofazimine
bedaquiline
mmpL5 775994 c.2485_2487delATCinsCG frameshift_variant&missense_variant 0.71 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776000 c.2479_2481delCTGinsAC frameshift_variant&missense_variant 0.77 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776005 p.Ile826Leu missense_variant 0.77 clofazimine
bedaquiline
mmpL5 776009 c.2472A>G synonymous_variant 0.77 clofazimine
bedaquiline
mmpL5 776030 c.2451G>T synonymous_variant 0.77 clofazimine
bedaquiline
rpsL 781682 c.123T>C synonymous_variant 0.64 streptomycin
rpsL 781709 c.150G>C synonymous_variant 0.77 streptomycin Not assoc w R - Interim
rpsL 781715 c.156T>C synonymous_variant 0.77 streptomycin
rpsL 781718 c.159C>G synonymous_variant 0.77 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.77 streptomycin
rpsL 781733 c.174G>C synonymous_variant 0.77 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.77 streptomycin
rpsL 781737 p.Gln60Gly missense_variant 0.77 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.77 streptomycin
rpsL 781751 c.192G>C synonymous_variant 0.77 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.77 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.71 streptomycin
rpsL 781766 c.207C>T synonymous_variant 0.71 streptomycin Not assoc w R - Interim
fbiC 1304613 c.1683T>C synonymous_variant 0.61 clofazimine
pretomanid
delamanid
fbiC 1304634 c.1704C>G synonymous_variant 0.65 clofazimine
pretomanid
delamanid
fbiC 1304640 c.1710A>C synonymous_variant 0.62 clofazimine
pretomanid
delamanid
fbiC 1304646 c.1716T>C synonymous_variant 0.62 clofazimine
pretomanid
delamanid
fbiC 1304652 c.1722C>G synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304658 c.1728C>G synonymous_variant 0.59 clofazimine
pretomanid
delamanid
fbiC 1304661 c.1731C>T synonymous_variant 0.56 clofazimine
pretomanid
delamanid
fbiC 1304670 c.1740G>C synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304671 p.Val581Thr missense_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304675 p.Gly582Asp missense_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304694 c.1764A>C synonymous_variant 0.62 clofazimine
pretomanid
delamanid
fbiC 1304703 c.1773C>G synonymous_variant 0.54 clofazimine
pretomanid
delamanid
fbiC 1304715 c.1785G>T synonymous_variant 0.54 clofazimine
pretomanid
delamanid
fbiC 1304724 c.1794A>G synonymous_variant 0.58 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304727 c.1797A>C synonymous_variant 0.57 clofazimine
pretomanid
delamanid
fbiC 1304736 c.1806G>A synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304739 c.1809C>A synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304748 c.1818T>C synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304751 c.1821C>G synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304757 c.1827A>G synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304760 c.1830G>C synonymous_variant 0.53 clofazimine
pretomanid
delamanid
sigE 1364919 c.507T>C synonymous_variant 0.73 pyrazinamide
sigE 1364922 p.Glu170Asp missense_variant 0.7 pyrazinamide
sigE 1364950 c.538_540delGCAinsTG frameshift_variant&stop_gained 0.82 pyrazinamide Uncertain significance
sigE 1364955 c.543G>A synonymous_variant 0.82 pyrazinamide
sigE 1364962 c.550_552delCCTinsGC frameshift_variant&missense_variant 0.73 pyrazinamide Uncertain significance
sigE 1364967 c.555C>T synonymous_variant 0.67 pyrazinamide
sigE 1364976 c.564T>C synonymous_variant 0.73 pyrazinamide Not assoc w R - Interim
sigE 1364980 c.568_570delTTGinsCC frameshift_variant&missense_variant 0.73 pyrazinamide Uncertain significance
sigE 1364984 p.Ala191Asp missense_variant 0.73 pyrazinamide
sigE 1364992 p.Pro194Ala missense_variant 0.73 pyrazinamide
sigE 1365003 c.591T>C synonymous_variant 0.73 pyrazinamide
sigE 1365006 c.594T>C synonymous_variant 0.73 pyrazinamide
sigE 1365015 c.603G>C synonymous_variant 0.67 pyrazinamide
sigE 1365018 c.606G>C synonymous_variant 0.67 pyrazinamide
sigE 1365042 c.630G>C synonymous_variant 0.67 pyrazinamide
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472848 n.1003T>A non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.86 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.72 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpsA 1833745 c.204G>C synonymous_variant 0.75 pyrazinamide
rpsA 1833772 c.231C>T synonymous_variant 0.88 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.94 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.94 pyrazinamide
rpsA 1833793 c.252C>T synonymous_variant 0.95 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.95 pyrazinamide
rpsA 1833808 c.267G>C synonymous_variant 0.95 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.95 pyrazinamide
rpsA 1833820 c.279G>A synonymous_variant 0.9 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.87 pyrazinamide
rpsA 1833838 c.297G>A synonymous_variant 0.87 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.82 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.77 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.75 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.79 pyrazinamide
rpsA 1833892 c.351G>A synonymous_variant 0.72 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.72 pyrazinamide
rpsA 1833904 c.363G>A synonymous_variant 0.65 pyrazinamide