TB-Profiler result

Run: ERR12015086
Summary

Run ID: ERR12015086

Sample name:

Date: 09-01-2024 00:22:02

Number of reads: 421868

Percentage reads mapped: 98.77

Strain: lineage4.8

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 (0.43)
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
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 0.43 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 7362 p.Glu21Gln missense_variant 1.0
rpoB 761015 c.1209G>C synonymous_variant 0.64
rpoB 761021 c.1215G>C synonymous_variant 0.64
rpoB 761027 c.1221A>G synonymous_variant 0.55
rpoB 761036 c.1230G>C synonymous_variant 0.55
rpoB 761037 c.1231T>C synonymous_variant 0.55
rpoB 761057 c.1251G>C synonymous_variant 0.5
rpoB 761102 c.1296A>G synonymous_variant 0.44
rpoB 761129 c.1323G>C synonymous_variant 0.32
rpoB 761133 c.1327_1329delTTGinsCTC synonymous_variant 0.32
rpoB 761645 c.1839C>G synonymous_variant 0.37
rpoB 761648 c.1842T>C synonymous_variant 0.37
rpoB 762053 c.2247T>C synonymous_variant 0.31
rpoB 762062 c.2256T>C synonymous_variant 0.31
rpoB 762065 c.2259T>C synonymous_variant 0.31
rpoB 762083 c.2277T>C synonymous_variant 0.32
rpoB 762086 c.2280G>C synonymous_variant 0.32
rpoB 762101 c.2295C>G synonymous_variant 0.34
rpoB 762114 p.Ile770Val missense_variant 0.35
rpoB 762131 c.2325C>G synonymous_variant 0.42
rpoB 762143 c.2337T>C synonymous_variant 0.35
rpoB 762149 c.2343G>C synonymous_variant 0.41
rpoB 762185 c.2379G>C synonymous_variant 0.37
rpoB 762221 c.2415G>A synonymous_variant 0.4
rpoB 762233 c.2427G>C synonymous_variant 0.41
rpoB 762254 c.2448T>C synonymous_variant 0.46
rpoB 762257 c.2451C>G synonymous_variant 0.5
rpoB 762284 c.2478G>T synonymous_variant 0.45
rpoB 762293 c.2487T>C synonymous_variant 0.45
rpoB 762296 c.2490G>C synonymous_variant 0.44
rpoB 762317 c.2511A>G synonymous_variant 0.35
rpoB 762329 c.2523G>C synonymous_variant 0.38
rpoC 763528 c.159G>A synonymous_variant 0.22
rpoC 763546 c.177A>G synonymous_variant 0.27
rpoC 763570 c.201G>C synonymous_variant 0.24
rpoC 763573 c.204G>C synonymous_variant 0.24
rpoC 763576 c.207C>G synonymous_variant 0.25
rpoC 763594 c.225C>T synonymous_variant 0.26
rpoC 763600 c.231C>T synonymous_variant 0.24
rpoC 763603 c.234C>T synonymous_variant 0.25
rpoC 763636 c.267T>C synonymous_variant 0.26
rpoC 763660 c.291T>G synonymous_variant 0.23
rpoC 763696 c.327T>C synonymous_variant 0.17
rpoC 763702 c.333C>G synonymous_variant 0.17
rpoC 764112 p.Tyr248Phe missense_variant 0.27
rpoC 764116 c.747C>T synonymous_variant 0.27
rpoC 764131 c.762T>C synonymous_variant 0.25
rpoC 764188 c.819A>G synonymous_variant 0.24
rpoC 764195 p.Ser276Ile missense_variant 0.24
rpoC 764203 c.834G>C synonymous_variant 0.23
rpoC 764206 c.837T>C synonymous_variant 0.23
rpoC 764215 c.846A>G synonymous_variant 0.24
rpoC 764536 c.1167G>C synonymous_variant 0.47
rpoC 764539 c.1170C>G synonymous_variant 0.47
rpoC 764554 c.1185C>T synonymous_variant 0.44
rpoC 764560 c.1191T>C synonymous_variant 0.44
rpoC 764566 c.1197C>G synonymous_variant 0.44
rpoC 764593 c.1224C>T synonymous_variant 0.32
rpoC 764650 c.1281G>T synonymous_variant 0.29
rpoC 764872 c.1503A>G synonymous_variant 0.38
rpoC 764888 c.1519T>C synonymous_variant 0.44
rpoC 764932 c.1563C>G synonymous_variant 0.44
rpoC 764948 c.1579T>C synonymous_variant 0.47
rpoC 764968 c.1599T>C synonymous_variant 0.37
rpoC 764995 c.1626C>G synonymous_variant 0.35
rpoC 766573 c.3204T>C synonymous_variant 0.67
rpoC 766630 c.3261G>T synonymous_variant 0.55
rpoC 766657 c.3288A>G synonymous_variant 0.46
rpoC 766660 c.3291G>C synonymous_variant 0.46
rpoC 766666 c.3297C>T synonymous_variant 0.54
rpoC 766672 c.3303T>C synonymous_variant 0.54
rpoC 766690 c.3321G>C synonymous_variant 0.54
rpoC 766693 c.3324C>T synonymous_variant 0.55
rpoC 766711 c.3342C>T synonymous_variant 0.48
rpoC 766726 c.3357T>C synonymous_variant 0.55
rpoC 766738 c.3369G>C synonymous_variant 0.53
rpoC 766765 c.3396A>C synonymous_variant 0.52
rpoC 766774 c.3405T>C synonymous_variant 0.55
rpoC 766801 c.3432C>A synonymous_variant 0.47
rpoC 766804 c.3435A>G synonymous_variant 0.47
rpoC 766807 c.3438T>C synonymous_variant 0.47
rpoC 766861 c.3492G>C synonymous_variant 0.54
rpoC 766864 c.3495G>C synonymous_variant 0.54
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781892 c.333A>G synonymous_variant 0.35
rpsL 781898 c.339A>T synonymous_variant 0.33
rpsL 781916 c.357T>C synonymous_variant 0.38
rpsL 781929 p.Gly124Ser missense_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.17
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.17
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.42
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.42
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.41
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.41
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.16
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.23
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.21
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.27
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.73
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.21
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.13
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.14
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.15
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.15
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.2
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.2
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.17
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.27
rrl 1474282 n.625G>A non_coding_transcript_exon_variant 0.25
rrl 1474288 n.632_634delCTT non_coding_transcript_exon_variant 0.22
rrl 1474294 n.638_649delCTCTCCGGAGGA non_coding_transcript_exon_variant 0.24
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.23
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.23
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.34
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.33
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.36
rrl 1474409 n.756_766delACCCACACGCG non_coding_transcript_exon_variant 0.35
rrl 1474427 n.770A>C non_coding_transcript_exon_variant 0.34
rrl 1474429 n.772G>C non_coding_transcript_exon_variant 0.34
rrl 1474431 n.774_775delGCinsTTTGGG non_coding_transcript_exon_variant 0.33
rrl 1474435 n.780_783delGAAT non_coding_transcript_exon_variant 0.35
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.59
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.53
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.51
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.5
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.47
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.3
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.33
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.43
rrl 1475028 n.1371G>A non_coding_transcript_exon_variant 0.36
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.28
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.35
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.24
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.24
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.26
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.26
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.26
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.26
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.22
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.23
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.18
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.17
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.18
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.19
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.26
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.23
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.16
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.19
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.2
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.2
rrl 1475758 n.2104delC non_coding_transcript_exon_variant 0.32
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.38
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.41
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.27
rrl 1476034 n.2377C>A non_coding_transcript_exon_variant 0.12
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.12
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.15
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.15
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.21
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.21
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.22
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.19
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.18
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.18
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.19
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.19
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.17
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.16
rrl 1476732 n.3075T>C non_coding_transcript_exon_variant 0.13
rpsA 1833667 c.126C>G synonymous_variant 0.13
rpsA 1833703 c.162C>T synonymous_variant 0.13
rpsA 1833724 c.183C>G synonymous_variant 0.2
rpsA 1833727 c.186G>C synonymous_variant 0.2
rpsA 1833745 c.204G>C synonymous_variant 0.17
rpsA 1833874 c.333T>C synonymous_variant 0.23
rpsA 1833928 c.387G>C synonymous_variant 0.35
rpsA 1833971 c.430C>T synonymous_variant 0.37
rpsA 1833979 c.438T>C synonymous_variant 0.36
rpsA 1834000 c.459G>C synonymous_variant 0.31
rpsA 1834021 c.480C>T synonymous_variant 0.2
rpsA 1834030 c.489C>G synonymous_variant 0.23
rpsA 1834222 c.681T>C synonymous_variant 0.27
rpsA 1834249 c.708T>C synonymous_variant 0.26
rpsA 1834261 c.720A>G synonymous_variant 0.29
rpsA 1834264 c.723G>C synonymous_variant 0.29
rpsA 1834294 c.753G>T synonymous_variant 0.27
rpsA 1834297 c.756C>T synonymous_variant 0.3
rpsA 1834303 c.762T>C synonymous_variant 0.3
rpsA 1834306 c.765T>C synonymous_variant 0.34
rpsA 1834654 p.Glu371Asp missense_variant 0.29
rpsA 1834717 c.1176C>T synonymous_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3877656 c.852T>C synonymous_variant 0.47
rpoA 3877668 c.840A>G synonymous_variant 0.43
rpoA 3877677 p.Ala277Ser missense_variant 0.41
rpoA 3877680 c.828G>C synonymous_variant 0.41
rpoA 3877686 c.822A>G synonymous_variant 0.43
rpoA 3877692 c.816G>C synonymous_variant 0.43
rpoA 3877704 c.804G>C synonymous_variant 0.39
rpoA 3877737 c.771G>C synonymous_variant 0.35
rpoA 3877770 c.738A>G synonymous_variant 0.39
rpoA 3877776 c.732T>C synonymous_variant 0.37
rpoA 3877782 c.726T>C synonymous_variant 0.35
clpC1 4038530 p.Glu725Asp missense_variant 0.38
clpC1 4038587 c.2118C>T synonymous_variant 0.42
clpC1 4038596 c.2109A>G synonymous_variant 0.56
clpC1 4038602 c.2103G>C synonymous_variant 0.57
clpC1 4038623 c.2082A>G synonymous_variant 0.62
clpC1 4038640 p.Asp689Asn missense_variant 0.65
clpC1 4038653 c.2052C>T synonymous_variant 0.61
clpC1 4038656 p.Lys683Gln missense_variant 0.59
clpC1 4038661 p.Ser682Thr missense_variant 0.59
clpC1 4038662 c.2043T>C synonymous_variant 0.61
clpC1 4038671 c.2034T>C synonymous_variant 0.62
clpC1 4038683 c.2022T>C synonymous_variant 0.59
clpC1 4038695 c.2010C>G synonymous_variant 0.58
clpC1 4038701 c.2004G>C synonymous_variant 0.61
clpC1 4038704 c.2001T>C synonymous_variant 0.59
clpC1 4038707 c.1998C>G synonymous_variant 0.59
clpC1 4038710 c.1995G>C synonymous_variant 0.58
clpC1 4038713 c.1992T>C synonymous_variant 0.56
clpC1 4038740 c.1965G>C synonymous_variant 0.59
clpC1 4038755 c.1950G>T synonymous_variant 0.54
clpC1 4038773 c.1932T>C synonymous_variant 0.56
clpC1 4038782 c.1923G>C synonymous_variant 0.53
clpC1 4038790 c.1915C>T synonymous_variant 0.52
clpC1 4038812 c.1893T>C synonymous_variant 0.58
clpC1 4038815 c.1890G>C synonymous_variant 0.56
clpC1 4038863 c.1842G>C synonymous_variant 0.62
clpC1 4038878 c.1827A>G synonymous_variant 0.66
clpC1 4038908 c.1797C>G synonymous_variant 0.69
clpC1 4038914 c.1791G>C synonymous_variant 0.69
clpC1 4038923 c.1780_1782delCTAinsTTG synonymous_variant 0.75
clpC1 4038953 c.1752A>G synonymous_variant 0.68
clpC1 4038965 c.1740T>C synonymous_variant 0.52
clpC1 4038971 c.1734T>C synonymous_variant 0.35
clpC1 4038974 c.1731T>C synonymous_variant 0.33
clpC1 4038989 c.1716T>C synonymous_variant 0.39
clpC1 4038997 c.1708T>C synonymous_variant 0.39
clpC1 4039022 c.1683A>G synonymous_variant 0.37
clpC1 4039025 c.1680C>G synonymous_variant 0.27
clpC1 4039037 c.1668T>C synonymous_variant 0.23
clpC1 4039064 c.1641C>T synonymous_variant 0.31
panD 4044017 p.Ala89Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245578 c.-936G>A upstream_gene_variant 1.0
ethA 4328338 c.-865G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0