TB-Profiler result

Run: SRR7068873
Summary

Run ID: SRR7068873

Sample name:

Date: 2024-05-20T09:11:24.167829

Number of reads: 1705037

Percentage reads mapped: 77.77

Median coverage: 56.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 1.0
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 rrs n.888G>A Uncertain significance Mutation from literature
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance Mutation from literature
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
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
dnaA 1139 p.Thr380Ile missense_variant 0.15 isoniazid Uncertain significance
gyrB 4975 c.-265G>A upstream_gene_variant 0.1 moxifloxacin
levofloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
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
atpE 1460992 c.-53A>C upstream_gene_variant 1.0 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.66 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472675 n.830_832delTCCinsCCT non_coding_transcript_exon_variant 0.65 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.19 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.15 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472682 n.837_842delTTGGGAinsGGGAC non_coding_transcript_exon_variant 0.48 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.79 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.69 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.52 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.58 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Not assoc w R
capreomycin Not assoc w R
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.41 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.67 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.44 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin
capreomycin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrl 1474634 n.977T>C non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid
rrl 1474674 n.1017_1018delACinsG non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1475760 n.2103_2108delCCGCAAinsTCTTTT non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.44 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.63 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2170412 c.201G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288982 p.Thr87Met missense_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv3083 3448508 c.6_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
embC 4241554 c.1692G>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326617 p.Tyr286Ala missense_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R