TB-Profiler result

Run: SRR8692897
Summary

Run ID: SRR8692897

Sample name:

Date: 13-08-2023 20:03:46

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.9

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
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 0.99
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 0.84 linezolid
pncA 2289039 p.Trp68Leu missense_variant 0.13 pyrazinamide
pncA 2289073 p.His57Asp missense_variant 0.12 pyrazinamide
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 5308 c.69G>A synonymous_variant 0.33
gyrB 6196 c.957C>G synonymous_variant 0.12
gyrB 6202 c.963C>G synonymous_variant 0.13
gyrB 6203 p.Ser322Ala missense_variant 0.13
gyrB 6214 c.975G>C synonymous_variant 0.12
gyrB 6215 p.Ser326Thr missense_variant 0.12
gyrB 6223 c.984G>C synonymous_variant 0.12
gyrB 6243 p.Arg335Gln missense_variant 0.12
gyrB 6250 c.1011A>G synonymous_variant 0.11
gyrB 6253 c.1014G>C synonymous_variant 0.11
gyrB 6365 p.Gly376Cys missense_variant 0.2
gyrA 8013 p.Gln238Lys missense_variant 0.17
gyrA 9230 c.1929T>C synonymous_variant 0.11
gyrA 9275 c.1974G>A synonymous_variant 0.12
gyrA 9296 c.1995T>C synonymous_variant 0.12
gyrA 9299 c.1998G>C synonymous_variant 0.13
gyrA 9304 p.Gly668Glu missense_variant 0.18
gyrA 9311 c.2010C>T synonymous_variant 0.12
gyrA 9324 c.2023_2025delTCGinsAGC synonymous_variant 0.13
gyrA 9335 c.2034G>T synonymous_variant 0.12
gyrA 9345 c.2044A>C synonymous_variant 0.12
fgd1 491245 p.Tyr155His missense_variant 0.1
fgd1 491728 p.Asp316Tyr missense_variant 0.15
rpoB 760019 c.213G>T synonymous_variant 0.13
rpoB 760235 c.429T>C synonymous_variant 0.15
rpoB 760244 c.438G>C synonymous_variant 0.15
rpoB 760256 c.450C>T synonymous_variant 0.15
rpoB 760283 c.477G>C synonymous_variant 0.17
rpoC 762443 c.-927G>C upstream_gene_variant 0.1
rpoC 762449 c.-921C>G upstream_gene_variant 0.11
rpoC 762452 c.-918G>C upstream_gene_variant 0.1
rpoC 763594 c.225C>T synonymous_variant 0.16
rpoC 763633 c.264T>C synonymous_variant 0.23
rpoC 763660 c.291T>G synonymous_variant 0.22
rpoC 763696 c.327T>C synonymous_variant 0.17
rpoC 763699 c.330G>C synonymous_variant 0.18
rpoC 763702 c.333C>G synonymous_variant 0.19
rpoC 763708 c.339G>C synonymous_variant 0.19
rpoC 763709 c.340C>T synonymous_variant 0.19
rpoC 763714 c.345G>C synonymous_variant 0.18
rpoC 763717 c.348T>C synonymous_variant 0.18
rpoC 763726 c.357C>T synonymous_variant 0.18
rpoC 763747 c.378G>A synonymous_variant 0.12
rpoC 764371 c.1002G>C synonymous_variant 0.12
rpoC 764377 c.1008C>G synonymous_variant 0.12
rpoC 764380 c.1011G>C synonymous_variant 0.13
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.12
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.14
rpoC 764410 c.1041G>C synonymous_variant 0.13
rpoC 764431 c.1062G>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.14
rpoC 764435 c.1066_1068delAGGinsCGA synonymous_variant 0.14
rpoC 766242 p.Thr958Asn missense_variant 0.12
rpoC 767098 c.3729T>C synonymous_variant 0.12
rpoC 767104 c.3735C>G synonymous_variant 0.14
rpoC 767106 p.Asn1246Met missense_variant 0.14
rpoC 767119 c.3750A>G synonymous_variant 0.23
rpoC 767155 c.3786C>G synonymous_variant 0.24
rpoC 767162 p.Asn1265Ala missense_variant 0.19
rpoC 767173 c.3804C>G synonymous_variant 0.17
rpoC 767174 p.Asn1269Asp missense_variant 0.17
rpoC 767180 p.Ala1271Gln missense_variant 0.14
rpoC 767185 c.3816G>C synonymous_variant 0.13
rpoC 767186 p.Gln1273Asn missense_variant 0.13
rpoC 767191 c.3822C>G synonymous_variant 0.12
rpoC 767197 c.3828G>A synonymous_variant 0.12
rpoC 767221 c.3852C>G synonymous_variant 0.15
rpoC 767230 c.3861G>C synonymous_variant 0.11
rpoC 767233 c.3864T>C synonymous_variant 0.1
mmpL5 776210 c.2271C>T synonymous_variant 0.12
mmpL5 776591 c.1890C>A synonymous_variant 0.12
mmpL5 776734 p.Ser583Gly missense_variant 0.11
mmpL5 777042 p.Arg480Leu missense_variant 0.2
mmpL5 777083 p.Asn466Lys missense_variant 0.15
mmpL5 778747 c.-267C>A upstream_gene_variant 0.15
mmpS5 779509 c.-604G>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 0.11
rplC 800651 c.-158G>C upstream_gene_variant 0.15
Rv1258c 1406686 p.Val219Ile missense_variant 0.84
atpE 1460952 c.-93T>C upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471834 n.-12G>T upstream_gene_variant 0.18
rrs 1471979 n.134T>C non_coding_transcript_exon_variant 0.2
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.22
rrs 1472040 n.195T>G non_coding_transcript_exon_variant 0.22
rrs 1472043 n.198T>G non_coding_transcript_exon_variant 0.22
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.29
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.38
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.45
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.45
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.6
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.58
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.5
rrs 1472289 n.444T>C non_coding_transcript_exon_variant 0.5
rrs 1472290 n.445C>A non_coding_transcript_exon_variant 0.5
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 0.5
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.4
rrs 1472324 n.479G>T non_coding_transcript_exon_variant 0.47
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.54
rrs 1472337 n.492C>G non_coding_transcript_exon_variant 0.47
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.48
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.44
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.47
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.4
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.5
rrs 1472573 n.728C>A non_coding_transcript_exon_variant 0.14
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.4
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.33
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 0.33
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.33
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.33
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.31
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.31
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.31
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.33
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.22
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.22
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.24
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.24
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.21
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.22
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.22
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.21
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.21
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.15
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.14
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.14
rrs 1473165 n.1320C>T non_coding_transcript_exon_variant 0.22
rrs 1473239 n.1394G>T non_coding_transcript_exon_variant 0.25
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.29
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.25
rrl 1473731 n.74T>A non_coding_transcript_exon_variant 0.18
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.17
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.17
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.18
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.25
rrl 1473811 n.154C>A non_coding_transcript_exon_variant 0.25
rrl 1473814 n.157A>C non_coding_transcript_exon_variant 0.25
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.25
rrl 1473816 n.159C>G non_coding_transcript_exon_variant 0.25
rrl 1473961 n.304G>T non_coding_transcript_exon_variant 0.13
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.25
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.25
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.3
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.3
rrl 1474185 n.528G>A non_coding_transcript_exon_variant 0.33
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.56
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.2
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.2
rrl 1474340 n.683C>A non_coding_transcript_exon_variant 0.15
rrl 1474792 n.1135C>A non_coding_transcript_exon_variant 0.2
rrl 1474895 n.1238C>A non_coding_transcript_exon_variant 0.12
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.27
rrl 1475108 n.1451C>G non_coding_transcript_exon_variant 0.5
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.25
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.25
rrl 1475209 n.1552G>A non_coding_transcript_exon_variant 0.18
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.18
rrl 1475221 n.1564C>G non_coding_transcript_exon_variant 0.18
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.29
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.29
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.29
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.33
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.22
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.2
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.2
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.2
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.2
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.17
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.46
rrl 1475759 n.2102C>T non_coding_transcript_exon_variant 0.46
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.46
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.46
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.5
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.5
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.58
rrl 1475961 n.2304C>A non_coding_transcript_exon_variant 0.2
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.25
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.22
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.25
rrl 1476003 n.2346T>A non_coding_transcript_exon_variant 0.29
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.29
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.29
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.29
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.29
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.29
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.29
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.29
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.29
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.29
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.29
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.25
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.29
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.57
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.57
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.62
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.7
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.68
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.68
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.68
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.59
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.59
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.12
rrl 1476512 n.2855C>A non_coding_transcript_exon_variant 0.18
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.18
rrl 1476576 n.2919C>A non_coding_transcript_exon_variant 0.33
rrl 1476777 n.3120C>A non_coding_transcript_exon_variant 0.22
inhA 1673387 c.-815C>A upstream_gene_variant 0.13
rpsA 1833616 c.75A>G synonymous_variant 0.14
rpsA 1833619 c.78A>C synonymous_variant 0.14
rpsA 1833625 c.84A>G synonymous_variant 0.14
rpsA 1833628 c.87G>C synonymous_variant 0.14
rpsA 1833676 c.135A>G synonymous_variant 0.2
rpsA 1834213 c.672G>C synonymous_variant 0.17
rpsA 1834231 c.690T>C synonymous_variant 0.15
rpsA 1834234 c.693G>C synonymous_variant 0.14
rpsA 1834240 c.699T>C synonymous_variant 0.14
rpsA 1834249 c.708T>C synonymous_variant 0.13
rpsA 1834261 c.720A>G synonymous_variant 0.12
rpsA 1834264 c.723G>C synonymous_variant 0.12
rpsA 1834279 c.738C>T synonymous_variant 0.12
rpsA 1834294 c.753G>C synonymous_variant 0.13
rpsA 1834299 p.Gln253Pro missense_variant 0.11
rpsA 1834303 c.762T>C synonymous_variant 0.11
rpsA 1834306 c.765T>C synonymous_variant 0.11
rpsA 1834585 c.1044C>A synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 0.14
PPE35 2168872 c.1741C>T synonymous_variant 0.13
PPE35 2168912 c.1701G>T synonymous_variant 0.17
PPE35 2168939 p.Leu558Phe missense_variant 0.14
PPE35 2169866 c.747G>T synonymous_variant 0.17
Rv1979c 2222020 p.Arg382Gln missense_variant 0.14
Rv1979c 2222257 p.Ile303Thr missense_variant 0.13
Rv1979c 2222391 c.774C>A synonymous_variant 0.18
Rv1979c 2222541 c.624T>C synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.32
eis 2715415 c.-83C>A upstream_gene_variant 0.12
ald 3086697 c.-123G>T upstream_gene_variant 0.29
fbiB 3642858 p.Ala442Thr missense_variant 0.13
clpC1 4038623 c.2082A>G synonymous_variant 0.11
clpC1 4038956 c.1749T>C synonymous_variant 0.1
clpC1 4039463 c.1242C>G synonymous_variant 0.11
clpC1 4039466 c.1239T>C synonymous_variant 0.11
clpC1 4039469 c.1236T>C synonymous_variant 0.12
clpC1 4039472 c.1233G>C synonymous_variant 0.12
clpC1 4039934 c.771G>C synonymous_variant 0.12
clpC1 4039937 c.768G>C synonymous_variant 0.12
clpC1 4040666 c.39C>A synonymous_variant 0.15
embC 4241806 c.1944G>A synonymous_variant 0.14
embA 4245152 c.1920C>A synonymous_variant 0.13
aftB 4267084 p.His585Asn missense_variant 0.12
ethA 4327173 p.His101Asn missense_variant 0.18