TB-Profiler result

Run: ERR9786528
Summary

Run ID: ERR9786528

Sample name:

Date: 2024-10-05T10:11:01.618333

Number of reads: 1114197

Percentage reads mapped: 81.46

Median coverage: 46.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 1.0
lineage4.6.2 Euro-American RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) RD726 1.0
lineage4 Euro-American None 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
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 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764254 c.885G>A synonymous_variant 0.2 rifampicin
rpoC 764263 c.894G>C synonymous_variant 0.2 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.2 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764284 c.915G>C synonymous_variant 0.2 rifampicin
rpoC 764297 p.Met310Leu missense_variant 0.18 rifampicin
rpoC 764320 c.951C>G synonymous_variant 0.17 rifampicin
rpoC 764341 c.972G>C synonymous_variant 0.15 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.15 rifampicin
rpoC 764407 p.Arg346Ser missense_variant 0.11 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764437 c.1068G>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.14 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.14 rifampicin
rpoC 764455 c.1086G>A synonymous_variant 0.16 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764500 c.1131C>G synonymous_variant 0.18 rifampicin
rpoC 764503 c.1134G>C synonymous_variant 0.17 rifampicin
rpoC 764509 c.1140G>T synonymous_variant 0.21 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764545 c.1176C>G synonymous_variant 0.18 rifampicin
rpoC 764548 c.1179G>A synonymous_variant 0.2 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.21 rifampicin
rpoC 764602 c.1233C>T synonymous_variant 0.19 rifampicin
rpoC 764605 c.1236G>T synonymous_variant 0.17 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764686 c.1317C>T synonymous_variant 0.16 rifampicin
rpoC 764701 c.1332C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>A synonymous_variant 0.14 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764749 c.1380G>C synonymous_variant 0.12 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764764 p.His465Gln missense_variant 0.16 rifampicin
rpoC 764767 c.1398G>A synonymous_variant 0.18 rifampicin
rpoC 764797 c.1428G>C synonymous_variant 0.18 rifampicin
rpoC 764803 c.1434C>G synonymous_variant 0.17 rifampicin
rpoC 764812 p.Gln482Ala missense_variant 0.16 rifampicin
rpoC 764824 c.1455T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764863 c.1494G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764869 c.1500C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.12 rifampicin
rpoC 764902 c.1533C>G synonymous_variant 0.11 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.12 rifampicin
rpoC 764912 p.Met515Leu missense_variant 0.12 rifampicin
rpoC 764917 c.1548G>C synonymous_variant 0.12 rifampicin
rpoC 764920 c.1551G>C synonymous_variant 0.12 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.13 rifampicin
rpoC 764939 c.1570C>T synonymous_variant 0.13 rifampicin
rpoC 764948 c.1579_1581delTTGinsCTC synonymous_variant 0.12 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472497 n.652G>A non_coding_transcript_exon_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.13 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.13 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473828 n.171_172insCT non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1473835 n.179delA non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473844 n.187C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474721 n.1064G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474722 n.1065T>G non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474740 n.1083G>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474747 n.1090C>G non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476105 n.2450delA non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833838 c.297G>C synonymous_variant 0.12 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.12 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.14 pyrazinamide
rpsA 1833904 c.363G>A synonymous_variant 0.13 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833961 c.420C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.12 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.12 pyrazinamide
rpsA 1833985 c.444G>C synonymous_variant 0.11 pyrazinamide
rpsA 1833988 c.447C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833991 c.450C>A synonymous_variant 0.12 pyrazinamide
rpsA 1833997 c.456G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834327 c.786G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834357 c.816T>G synonymous_variant 0.12 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>A synonymous_variant 0.12 pyrazinamide
rpsA 1834552 c.1011G>T synonymous_variant 0.2 pyrazinamide
rpsA 1834555 c.1014T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834600 c.1059G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834612 c.1071G>T synonymous_variant 0.14 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063187 c.1542C>T synonymous_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.97 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2996208 p.Ala35Asp missense_variant 1.0 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 1.0 para-aminosalicylic_acid
Rv3083 3448567 p.His22Asp missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612571 c.546C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
rpoA 3877629 c.879C>G synonymous_variant 0.15 rifampicin
rpoA 3877656 c.852T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
clpC1 4039654 p.Thr351Ser missense_variant 0.17 pyrazinamide
clpC1 4039661 c.1044T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039664 c.1041G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039670 c.1035G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039682 c.1023C>G synonymous_variant 0.12 pyrazinamide
embC 4242550 c.2688C>G synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 1.0 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin