TB-Profiler result

Run: ERR4872102
Summary

Run ID: ERR4872102

Sample name:

Date: 01-04-2023 21:21:44

Number of reads: 4199859

Percentage reads mapped: 90.75

Strain: lineage4.6.4

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.4 Euro-American T;LAM None 0.98
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
rpoB 761155 p.Ser450Leu missense_variant 0.89 rifampicin
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.26 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289207 p.Asp12Ala missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
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
gyrB 6274 c.1035C>G synonymous_variant 0.14
gyrB 6286 c.1047T>C synonymous_variant 0.15
gyrB 6292 c.1053G>C synonymous_variant 0.14
gyrB 6295 c.1056A>G synonymous_variant 0.15
gyrA 6307 c.-995T>G upstream_gene_variant 0.14
gyrA 6325 c.-977C>G upstream_gene_variant 0.15
gyrA 6730 c.-572A>G upstream_gene_variant 0.15
gyrA 6742 c.-560A>G upstream_gene_variant 0.14
gyrA 6745 c.-557T>G upstream_gene_variant 0.14
gyrA 6824 c.-478C>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.3
rpoB 760181 c.375T>C synonymous_variant 0.2
rpoB 760184 c.378A>G synonymous_variant 0.19
rpoB 760196 c.390C>G synonymous_variant 0.22
rpoB 760223 c.417T>C synonymous_variant 0.2
rpoB 760235 c.429T>C synonymous_variant 0.22
rpoB 760253 c.447T>C synonymous_variant 0.19
rpoB 760283 c.477G>C synonymous_variant 0.18
rpoB 760307 c.501T>C synonymous_variant 0.15
rpoB 760376 p.Asp190Glu missense_variant 0.15
rpoC 763115 c.-255T>C upstream_gene_variant 0.16
rpoC 763148 c.-222G>C upstream_gene_variant 0.16
rpoC 763158 c.-212C>T upstream_gene_variant 0.16
rpoC 763456 c.87A>G synonymous_variant 0.15
rpoC 763468 c.99G>C synonymous_variant 0.18
rpoC 763486 c.117T>C synonymous_variant 0.15
rpoC 763528 c.159G>A synonymous_variant 0.17
rpoC 763546 c.177A>G synonymous_variant 0.17
rpoC 763570 c.201G>C synonymous_variant 0.15
rpoC 765583 c.2214G>T synonymous_variant 0.13
rpoC 765658 c.2289C>T synonymous_variant 0.17
rpoC 765700 c.2331T>C synonymous_variant 0.16
rpoC 765739 c.2370G>C synonymous_variant 0.15
rpoC 765772 c.2403C>G synonymous_variant 0.15
rpoC 765784 c.2415C>G synonymous_variant 0.14
rpoC 765796 c.2427C>T synonymous_variant 0.14
rpoC 766488 p.Pro1040Gln missense_variant 0.91
rpoC 767009 p.Ser1214Thr missense_variant 0.14
rpoC 767098 c.3729T>C synonymous_variant 0.16
rpoC 767119 c.3750A>G synonymous_variant 0.14
rpoC 767181 p.Ala1271Glu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775733 c.2748C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781736 c.177T>C synonymous_variant 0.14
rplC 800612 c.-197A>G upstream_gene_variant 0.15
rplC 800618 c.-191T>C upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.17
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.18
rrs 1472028 n.183A>T non_coding_transcript_exon_variant 0.23
rrs 1472030 n.185G>A non_coding_transcript_exon_variant 0.22
rrs 1472031 n.186G>A non_coding_transcript_exon_variant 0.23
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.21
rrs 1472044 n.199G>C non_coding_transcript_exon_variant 0.22
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.23
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.23
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.28
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.33
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.34
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.33
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.34
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.37
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.37
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.37
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.3
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.33
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.33
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.35
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.33
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.3
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.35
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.36
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.35
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.38
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.38
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.39
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.47
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.47
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.54
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.54
rrl 1474051 n.394T>C non_coding_transcript_exon_variant 0.5
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.49
rrl 1474056 n.399T>C non_coding_transcript_exon_variant 0.49
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.52
rrl 1474104 n.447G>A non_coding_transcript_exon_variant 0.51
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.52
rrl 1474112 n.455T>A non_coding_transcript_exon_variant 0.52
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.52
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.47
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.38
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.56
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.55
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.56
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.65
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.65
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.58
rrl 1474409 n.756_766delACCCACACGCG non_coding_transcript_exon_variant 0.39
rrl 1474427 n.770A>C non_coding_transcript_exon_variant 0.38
rrl 1474429 n.772G>C non_coding_transcript_exon_variant 0.38
rrl 1474435 n.780_783delGAAT non_coding_transcript_exon_variant 0.41
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.57
rrl 1474750 n.1093C>T non_coding_transcript_exon_variant 0.47
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.47
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.43
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.4
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.36
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.27
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.29
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.29
rrl 1474962 n.1306delG non_coding_transcript_exon_variant 0.3
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.34
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.45
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.49
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.55
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.53
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.46
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.44
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.43
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.42
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.46
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.44
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.45
rrl 1475271 n.1614A>C non_coding_transcript_exon_variant 0.46
rrl 1475273 n.1616T>A non_coding_transcript_exon_variant 0.44
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.45
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.45
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.49
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.54
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.55
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.61
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.66
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.69
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.71
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.7
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.71
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.67
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.69
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.69
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.62
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.63
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.58
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.59
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.5
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.59
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.51
rrl 1476025 n.2368G>T non_coding_transcript_exon_variant 0.57
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.55
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.59
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.57
rrl 1476034 n.2377C>A non_coding_transcript_exon_variant 0.57
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.65
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.62
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.62
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.63
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.62
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.62
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.57
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.59
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.59
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.61
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.28
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.26
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.29
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.3
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.27
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.26
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.27
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.27
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.27
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.29
rrl 1476723 n.3066T>A non_coding_transcript_exon_variant 0.27
rrl 1476725 n.3068C>T non_coding_transcript_exon_variant 0.23
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.23
rrl 1476732 n.3075T>C non_coding_transcript_exon_variant 0.22
rpsA 1833667 c.126C>G synonymous_variant 0.14
rpsA 1833724 c.183C>G synonymous_variant 0.19
rpsA 1833727 c.186G>C synonymous_variant 0.2
rpsA 1833742 c.201A>G synonymous_variant 0.21
rpsA 1833745 c.204G>C synonymous_variant 0.21
rpsA 1833787 c.246C>G synonymous_variant 0.22
rpsA 1833790 c.249T>A synonymous_variant 0.21
rpsA 1833799 c.258C>G synonymous_variant 0.24
rpsA 1833811 c.270G>C synonymous_variant 0.25
rpsA 1833838 c.297G>C synonymous_variant 0.23
rpsA 1833841 c.300C>G synonymous_variant 0.23
rpsA 1833847 c.306C>G synonymous_variant 0.22
rpsA 1833856 c.315A>G synonymous_variant 0.21
rpsA 1833862 c.321G>T synonymous_variant 0.22
rpsA 1833874 c.333T>C synonymous_variant 0.2
rpsA 1833928 c.387G>C synonymous_variant 0.24
rpsA 1833940 c.399C>G synonymous_variant 0.23
rpsA 1833970 c.429G>C synonymous_variant 0.19
rpsA 1833979 c.438T>C synonymous_variant 0.19
rpsA 1834000 c.459G>C synonymous_variant 0.18
rpsA 1834015 c.474G>C synonymous_variant 0.16
rpsA 1834021 c.480C>T synonymous_variant 0.16
rpsA 1834201 c.660C>T synonymous_variant 0.13
rpsA 1834222 c.681T>C synonymous_variant 0.14
rpsA 1834240 c.699T>C synonymous_variant 0.15
rpsA 1834297 c.756C>G synonymous_variant 0.14
rpsA 1834303 c.762T>G synonymous_variant 0.15
rpsA 1834306 c.765T>C synonymous_variant 0.15
rpsA 1834348 c.807T>C synonymous_variant 0.18
rpsA 1834366 c.825A>G synonymous_variant 0.16
rpsA 1834375 c.834G>A synonymous_variant 0.17
rpsA 1834396 c.855G>C synonymous_variant 0.16
rpsA 1834411 c.870T>C synonymous_variant 0.15
rpsA 1834417 c.876G>C synonymous_variant 0.16
rpsA 1834423 c.882G>C synonymous_variant 0.15
rpsA 1834435 c.894G>C synonymous_variant 0.15
rpsA 1834451 c.910T>C synonymous_variant 0.14
rpsA 1834558 c.1017C>G synonymous_variant 0.14
rpsA 1834594 c.1053C>T synonymous_variant 0.17
rpsA 1834606 c.1065C>G synonymous_variant 0.15
rpsA 1834609 c.1068T>C synonymous_variant 0.15
rpsA 1834622 p.Ser361Thr missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222795 p.Asp124Asn missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517947 c.-168C>T upstream_gene_variant 0.15
eis 2714393 p.Val314Leu missense_variant 1.0
Rv2752c 3065083 p.Val370Gly missense_variant 0.95
Rv2752c 3065997 c.195C>G synonymous_variant 0.14
Rv2752c 3066002 p.Met64Leu missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640412 c.-131G>A upstream_gene_variant 1.0
fbiB 3641526 c.-9A>C upstream_gene_variant 1.0
rpoA 3877962 c.546G>T synonymous_variant 0.14
rpoA 3877986 c.522G>C synonymous_variant 0.14
rpoA 3878385 c.123C>G synonymous_variant 0.15
rpoA 3878391 c.117T>C synonymous_variant 0.15
rpoA 3878396 c.112C>T synonymous_variant 0.16
clpC1 4039898 c.807C>G synonymous_variant 0.15
clpC1 4039904 c.801A>G synonymous_variant 0.16
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.17
clpC1 4039931 c.774T>C synonymous_variant 0.17
clpC1 4039946 c.759A>T synonymous_variant 0.16
clpC1 4039952 c.753T>C synonymous_variant 0.15
clpC1 4039958 c.747G>C synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embA 4245137 c.1905T>C synonymous_variant 0.14
embA 4245149 c.1917C>G synonymous_variant 0.14
embB 4246584 p.Arg24Pro missense_variant 0.35
embB 4248241 c.1728C>T synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407847 p.Ala119Asp missense_variant 1.0