TB-Profiler result

Run: SRR8692882
Summary

Run ID: SRR8692882

Sample name:

Date: 13-08-2023 21:33:05

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.9

Drug-resistance: HR-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
lineage4.9 Euro-American (H37Rv-like) T1 None 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
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid
katG 2155786 p.Ala109Val missense_variant 0.12 isoniazid
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 5615 p.Ser126Ala missense_variant 0.12
gyrB 6268 c.1029C>G synonymous_variant 0.11
gyrB 6295 c.1056A>G synonymous_variant 0.11
gyrA 6307 c.-995T>G upstream_gene_variant 0.11
gyrA 6310 c.-992G>C upstream_gene_variant 0.11
gyrA 6655 c.-647T>C upstream_gene_variant 0.11
gyrA 7404 p.Val35Met missense_variant 0.17
gyrA 8366 c.1065G>C synonymous_variant 0.12
gyrA 8382 p.Leu361Met missense_variant 0.12
gyrA 8393 c.1092T>C synonymous_variant 0.13
gyrA 8462 c.1161A>G synonymous_variant 0.11
gyrA 8486 c.1185T>C synonymous_variant 0.16
gyrA 8489 c.1188A>G synonymous_variant 0.11
gyrA 8504 c.1203G>C synonymous_variant 0.14
gyrA 8516 c.1215T>C synonymous_variant 0.13
gyrA 8520 c.1219C>T synonymous_variant 0.15
gyrA 8531 c.1230G>C synonymous_variant 0.12
gyrA 8536 p.Glu412Ala missense_variant 0.11
gyrA 8542 p.Val414Ala missense_variant 0.1
gyrA 8547 p.Ile416Val missense_variant 0.11
gyrA 8555 c.1254G>C synonymous_variant 0.11
gyrA 8557 p.Ala419Gly missense_variant 0.11
gyrA 8561 c.1260A>C synonymous_variant 0.1
gyrA 8567 p.Ile422Met missense_variant 0.11
gyrA 8603 c.1302A>C synonymous_variant 0.11
fgd1 491325 c.543G>T synonymous_variant 0.14
fgd1 491335 p.Ala185Ser missense_variant 0.14
mshA 576459 p.Ala371Val missense_variant 0.17
ccsA 620795 p.Ala302Asp missense_variant 0.13
rpoB 759844 p.Pro13His missense_variant 0.12
rpoB 760331 c.525G>T synonymous_variant 0.2
rpoB 760337 c.531C>G synonymous_variant 0.2
rpoB 760340 c.534G>C synonymous_variant 0.18
rpoB 760353 p.Glu183Ser missense_variant 0.18
rpoB 760356 p.Thr184Ser missense_variant 0.14
rpoB 760361 c.555T>C synonymous_variant 0.13
rpoB 760368 p.Ser188Ala missense_variant 0.12
rpoB 760376 p.Asp190Glu missense_variant 0.12
rpoB 760380 p.Thr192Asp missense_variant 0.12
rpoB 761051 c.1245G>T synonymous_variant 0.14
rpoB 761054 c.1248G>C synonymous_variant 0.13
rpoB 761057 c.1251G>C synonymous_variant 0.13
rpoB 761060 c.1254C>G synonymous_variant 0.13
rpoB 761063 c.1257C>G synonymous_variant 0.19
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.21
rpoB 761102 c.1296A>G synonymous_variant 0.2
rpoB 761132 c.1326G>T synonymous_variant 0.18
rpoB 761133 c.1327T>C synonymous_variant 0.18
rpoB 761147 c.1341C>T synonymous_variant 0.18
rpoB 761150 c.1344A>T synonymous_variant 0.18
rpoB 761165 c.1359G>C synonymous_variant 0.18
rpoB 761180 c.1374A>C synonymous_variant 0.16
rpoB 761189 c.1383T>C synonymous_variant 0.16
rpoB 761690 c.1884G>C synonymous_variant 0.11
rpoB 761693 c.1887G>C synonymous_variant 0.12
rpoB 761887 p.Gln694Arg missense_variant 0.11
rpoB 762137 c.2331C>T synonymous_variant 0.12
rpoB 762140 c.2334G>C synonymous_variant 0.12
rpoB 762143 c.2337T>C synonymous_variant 0.12
rpoB 762149 c.2343G>C synonymous_variant 0.12
rpoB 762156 p.Val784Ile missense_variant 0.13
rpoC 764346 p.Pro326Gln missense_variant 0.13
rpoC 764662 c.1293G>C synonymous_variant 0.12
rpoC 764677 c.1308C>G synonymous_variant 0.15
rpoC 764746 c.1377G>T synonymous_variant 0.15
rpoC 764752 c.1383G>C synonymous_variant 0.11
rpoC 764758 c.1389C>G synonymous_variant 0.11
rpoC 764764 c.1395T>C synonymous_variant 0.11
rpoC 765807 p.Gln813Arg missense_variant 0.1
rpoC 766055 p.Gly896Cys missense_variant 0.12
rpoC 766155 p.Ala929Glu missense_variant 0.14
rpoC 766344 p.Gly992Val missense_variant 0.14
rpoC 766351 c.2982C>A synonymous_variant 0.13
rpoC 766702 c.3333G>C synonymous_variant 0.1
rpoC 766712 p.Ser1115Ala missense_variant 0.12
rpoC 766720 c.3351C>T synonymous_variant 0.12
rpoC 766726 c.3357T>C synonymous_variant 0.12
rpoC 766738 c.3369G>T synonymous_variant 0.14
rpoC 766750 c.3381C>G synonymous_variant 0.17
rpoC 766765 c.3396A>C synonymous_variant 0.22
rpoC 766771 c.3402G>C synonymous_variant 0.25
rpoC 766774 c.3405T>C synonymous_variant 0.22
rpoC 766775 p.Arg1136Lys missense_variant 0.22
rpoC 766798 c.3429C>G synonymous_variant 0.22
rpoC 766804 c.3435A>G synonymous_variant 0.22
rpoC 766807 c.3438T>C synonymous_variant 0.22
rpoC 766840 c.3471C>A synonymous_variant 0.25
mmpL5 775749 p.Gly911Val missense_variant 0.14
mmpL5 776527 p.Met652Val missense_variant 0.11
rpsL 781640 p.Ser27Arg missense_variant 0.11
rpsL 781673 p.Tyr38* stop_gained 0.15
rplC 801333 c.525G>T synonymous_variant 0.22
fbiC 1304103 c.1173G>T synonymous_variant 0.12
fbiC 1305408 c.2478G>T synonymous_variant 0.25
Rv1258c 1406421 p.Phe307Ser missense_variant 0.12
Rv1258c 1406686 p.Val219Ile missense_variant 1.0
Rv1258c 1407050 c.291C>A synonymous_variant 0.2
embR 1416424 c.924C>A synonymous_variant 0.14
embR 1417238 p.Ala37Asp missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471866 n.21C>T non_coding_transcript_exon_variant 0.13
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.11
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.11
rrs 1471931 n.87delA non_coding_transcript_exon_variant 0.11
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.11
rrs 1471973 n.128C>A non_coding_transcript_exon_variant 0.12
rrs 1471979 n.134T>C non_coding_transcript_exon_variant 0.18
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.22
rrs 1472019 n.174G>A non_coding_transcript_exon_variant 0.15
rrs 1472023 n.178G>T non_coding_transcript_exon_variant 0.14
rrs 1472029 n.184C>T non_coding_transcript_exon_variant 0.15
rrs 1472030 n.185G>T non_coding_transcript_exon_variant 0.17
rrs 1472033 n.188A>C non_coding_transcript_exon_variant 0.15
rrs 1472035 n.190G>T non_coding_transcript_exon_variant 0.14
rrs 1472040 n.195T>G non_coding_transcript_exon_variant 0.13
rrs 1472043 n.198T>G non_coding_transcript_exon_variant 0.14
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.14
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.14
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.12
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.42
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.42
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.5
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.56
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.2
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.25
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 0.25
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.25
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.25
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.23
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.23
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.23
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.23
rrs 1472866 n.1021C>A non_coding_transcript_exon_variant 0.2
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.33
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.3
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.3
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.3
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.3
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.3
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.4
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.36
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.19
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.2
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.2
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.56
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.56
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.2
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.33
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.4
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.33
rrl 1473814 n.157A>C non_coding_transcript_exon_variant 0.36
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.36
rrl 1473816 n.159C>G non_coding_transcript_exon_variant 0.33
rrl 1473828 n.171G>C non_coding_transcript_exon_variant 0.4
rrl 1473829 n.172G>C non_coding_transcript_exon_variant 0.4
rrl 1473830 n.173T>G non_coding_transcript_exon_variant 0.4
rrl 1473831 n.174G>T non_coding_transcript_exon_variant 0.4
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.33
rrl 1473887 n.230T>A non_coding_transcript_exon_variant 0.33
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.33
rrl 1474034 n.377G>T non_coding_transcript_exon_variant 0.33
rrl 1474518 n.861C>A non_coding_transcript_exon_variant 0.15
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.36
rrl 1474669 n.1012G>T non_coding_transcript_exon_variant 0.17
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.27
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.27
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.25
rrl 1474709 n.1053delT non_coding_transcript_exon_variant 0.36
rrl 1474714 n.1058delT non_coding_transcript_exon_variant 0.36
rrl 1474749 n.1092C>A non_coding_transcript_exon_variant 0.13
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.4
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.36
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.42
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.45
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.4
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.33
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.4
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.25
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.25
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.25
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.25
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.33
rrl 1475759 n.2102C>T non_coding_transcript_exon_variant 0.29
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.29
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.29
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.29
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.29
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.38
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.25
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.28
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.3
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.33
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.35
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.35
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.35
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.46
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.46
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.46
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.46
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.46
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.44
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.47
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.47
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.47
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.47
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.5
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.5
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.36
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.24
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.25
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.23
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.23
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.21
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.18
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.17
rrl 1476404 n.2747G>A non_coding_transcript_exon_variant 0.13
rrl 1476430 n.2773G>T non_coding_transcript_exon_variant 0.23
rrl 1476439 n.2782G>T non_coding_transcript_exon_variant 0.15
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.5
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.4
fabG1 1674076 p.Thr213Ala missense_variant 0.11
rpsA 1833676 c.135A>G synonymous_variant 0.19
rpsA 1833679 c.138G>C synonymous_variant 0.18
rpsA 1833685 c.144G>T synonymous_variant 0.17
rpsA 1833694 c.153G>T synonymous_variant 0.17
rpsA 1833697 c.156C>G synonymous_variant 0.15
rpsA 1833703 c.162C>T synonymous_variant 0.14
rpsA 1833709 c.168C>T synonymous_variant 0.14
rpsA 1833727 c.186G>A synonymous_variant 0.17
rpsA 1833734 p.Ala65Ser missense_variant 0.17
rpsA 1833745 c.204G>C synonymous_variant 0.19
rpsA 1833760 c.219C>T synonymous_variant 0.18
rpsA 1833787 c.246C>G synonymous_variant 0.14
rpsA 1833790 c.249T>C synonymous_variant 0.14
rpsA 1833793 c.252C>T synonymous_variant 0.13
rpsA 1833802 c.261A>G synonymous_variant 0.12
rpsA 1834633 c.1092A>G synonymous_variant 0.11
rpsA 1834639 c.1098T>C synonymous_variant 0.11
rpsA 1834666 c.1125G>C synonymous_variant 0.14
rpsA 1834667 p.Ala376Ser missense_variant 0.14
rpsA 1834690 c.1149T>C synonymous_variant 0.14
rpsA 1834700 p.Gln387Ala missense_variant 0.15
rpsA 1834705 c.1164C>G synonymous_variant 0.15
rpsA 1834732 c.1191T>C synonymous_variant 0.12
rpsA 1834738 p.Glu399Asp missense_variant 0.12
rpsA 1834753 c.1212T>C synonymous_variant 0.14
rpsA 1834759 c.1218A>C synonymous_variant 0.14
rpsA 1834765 p.Glu408Asp missense_variant 0.14
rpsA 1834775 p.Ala412Thr missense_variant 0.14
ndh 2102464 c.579C>T synonymous_variant 0.2
PPE35 2170339 p.Val92Leu missense_variant 0.15
kasA 2518618 c.504G>T synonymous_variant 0.17
kasA 2518720 c.606C>A synonymous_variant 0.17
kasA 2518735 c.621C>A synonymous_variant 0.15
kasA 2518746 p.Ser211Tyr missense_variant 0.15
kasA 2518769 p.Arg219Ser missense_variant 0.15
folC 2746265 p.Ser445* stop_gained 0.13
folC 2746590 p.Gly337Cys missense_variant 0.15
pepQ 2859746 p.Leu225Met missense_variant 0.12
thyX 3067265 p.Phe227Leu missense_variant 0.13
fprA 3474083 p.Ala26Asp missense_variant 0.21
fprA 3475173 c.1169delA frameshift_variant 0.17
fprA 3475272 p.His422Gln missense_variant 0.15
whiB7 3568771 c.-92C>A upstream_gene_variant 0.15
whiB7 3568875 c.-196C>A upstream_gene_variant 0.12
fbiA 3640679 p.Asn46Ser missense_variant 0.12
fbiB 3641310 c.-225C>A upstream_gene_variant 0.14
alr 3840629 c.792C>G synonymous_variant 0.11
rpoA 3877591 p.Leu306Pro missense_variant 0.12
clpC1 4038180 p.Gly842Val missense_variant 0.17
clpC1 4038185 c.2520G>T synonymous_variant 0.17
clpC1 4038755 c.1950G>C synonymous_variant 0.14
clpC1 4038773 c.1932T>C synonymous_variant 0.17
clpC1 4038779 c.1926C>G synonymous_variant 0.18
clpC1 4038890 c.1815G>A synonymous_variant 0.17
clpC1 4039100 c.1605C>A synonymous_variant 0.13
clpC1 4039268 c.1437C>T synonymous_variant 0.13
clpC1 4039356 p.Leu450Pro missense_variant 0.12
clpC1 4040065 p.Leu214Met missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.12
clpC1 4040147 c.558A>G synonymous_variant 0.12
clpC1 4040153 c.552A>G synonymous_variant 0.12
clpC1 4040159 c.546G>C synonymous_variant 0.13
clpC1 4040162 c.543G>C synonymous_variant 0.13
clpC1 4040165 c.540G>C synonymous_variant 0.12
clpC1 4040168 c.537G>C synonymous_variant 0.12
clpC1 4040175 p.Asn177Ile missense_variant 0.12
clpC1 4040195 c.510G>C synonymous_variant 0.13
clpC1 4040200 c.505T>C synonymous_variant 0.12
clpC1 4040201 c.504C>A synonymous_variant 0.12
clpC1 4040204 c.501G>C synonymous_variant 0.12
clpC1 4040207 c.498T>G synonymous_variant 0.12
clpC1 4040213 p.Ser164Tyr missense_variant 0.12
clpC1 4040228 c.477G>C synonymous_variant 0.14
clpC1 4040237 c.468C>T synonymous_variant 0.15
embC 4239736 c.-127C>A upstream_gene_variant 0.12
embC 4242368 p.Arg836Ser missense_variant 0.15
embC 4242987 p.Ala1042Glu missense_variant 0.12
embA 4244201 p.Trp323Cys missense_variant 0.12
embA 4244317 p.Phe362Ser missense_variant 0.11
embA 4245977 p.Asp915Glu missense_variant 0.15
embB 4246760 p.Val83Met missense_variant 0.12
embB 4248542 p.Ala677Ser missense_variant 0.14
embB 4248934 p.Asn807Lys missense_variant 0.17
aftB 4267168 p.Gln557Lys missense_variant 0.13
ubiA 4269273 p.Met187Ile missense_variant 0.12
ethA 4326159 p.Val439Leu missense_variant 0.13
ethA 4326732 p.Ala248Ser missense_variant 0.14
ethR 4326742 c.-807C>A upstream_gene_variant 0.13
ethR 4326838 c.-711G>T upstream_gene_variant 0.13
ethR 4327441 c.-108G>T upstream_gene_variant 0.17
ethR 4327989 c.442delT frameshift_variant 0.13
ethA 4328061 c.-588C>A upstream_gene_variant 0.22
ethR 4328111 p.Ala188Val missense_variant 0.29
gid 4408153 p.Gly17Val missense_variant 0.15