TB-Profiler result

Run: SRR8692812
Summary

Run ID: SRR8692812

Sample name:

Date: 13-08-2023 19:22:55

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 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 0.13 linezolid
pncA 2289073 p.His57Asp missense_variant 0.13 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
gyrA 7814 c.513C>G synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 0.2
rpoB 760118 c.312T>G synonymous_variant 0.1
rpoB 760184 c.378A>G synonymous_variant 0.11
rpoB 760457 c.651C>T synonymous_variant 0.14
rpoB 760475 c.669A>G synonymous_variant 0.14
rpoB 760481 c.675G>T synonymous_variant 0.12
rpoB 760484 c.678A>G synonymous_variant 0.12
rpoB 760502 c.696C>G synonymous_variant 0.14
rpoB 760508 c.702G>C synonymous_variant 0.14
rpoB 760511 c.705G>C synonymous_variant 0.14
rpoB 760522 p.Ser239Asn missense_variant 0.14
rpoB 760567 p.Ser254Trp missense_variant 0.11
rpoB 760595 c.789C>A synonymous_variant 0.12
rpoB 761012 p.Asp402Glu missense_variant 0.12
rpoB 761217 p.Pro471Thr missense_variant 0.13
rpoB 761673 p.Gly623Trp missense_variant 0.14
rpoB 761990 c.2184G>C synonymous_variant 0.3
rpoB 761999 c.2193G>C synonymous_variant 0.33
rpoB 762002 c.2196C>G synonymous_variant 0.33
rpoB 762047 c.2241G>A synonymous_variant 0.4
rpoB 762053 c.2247T>C synonymous_variant 0.4
rpoB 762065 c.2259T>C synonymous_variant 0.33
rpoB 762083 c.2277T>C synonymous_variant 0.25
rpoB 762086 c.2280G>C synonymous_variant 0.25
rpoB 762101 c.2295C>G synonymous_variant 0.21
rpoB 762114 p.Ile770Val missense_variant 0.18
rpoB 762122 c.2316C>T synonymous_variant 0.14
rpoB 762131 c.2325C>G synonymous_variant 0.1
rpoC 763353 c.-17A>G upstream_gene_variant 0.11
rpoC 764521 c.1152T>C synonymous_variant 0.11
rpoC 764575 c.1206T>G synonymous_variant 0.13
rpoC 764611 c.1242G>T synonymous_variant 0.13
rpoC 764626 c.1257C>T synonymous_variant 0.14
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764650 c.1281G>T synonymous_variant 0.13
rpoC 764662 c.1293G>C synonymous_variant 0.1
rpoC 764677 c.1308C>G synonymous_variant 0.12
rpoC 764719 c.1350G>A synonymous_variant 0.14
rpoC 764746 c.1377G>T synonymous_variant 0.12
rpoC 764752 c.1383G>C synonymous_variant 0.12
rpoC 765952 c.2583G>C synonymous_variant 0.11
mmpL5 776433 p.Ser683* stop_gained 0.14
mmpL5 776878 p.Gln535Lys missense_variant 0.13
mmpL5 778021 p.Ala154Thr missense_variant 0.13
mmpS5 778820 p.Arg29Leu missense_variant 0.14
mmpR5 779474 p.Gly162Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 0.12
rpsL 781762 p.Pro68Leu missense_variant 0.13
rpsL 781857 p.Gly100Cys missense_variant 0.13
rpsL 781861 p.Ser101* stop_gained 0.13
rplC 801008 p.Thr67Lys missense_variant 0.12
fbiC 1305014 p.Thr695Lys missense_variant 0.15
Rv1258c 1406686 p.Val219Ile missense_variant 0.87
Rv1258c 1406699 p.Glu214Asp missense_variant 0.13
atpE 1460943 c.-102C>T upstream_gene_variant 0.17
atpE 1461099 p.Gly19Cys missense_variant 0.17
atpE 1461111 p.Gly23Cys missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471704 n.-142C>A upstream_gene_variant 0.14
rrs 1471774 n.-72G>T upstream_gene_variant 0.17
rrs 1471797 n.-49G>T upstream_gene_variant 0.29
rrs 1471817 n.-29G>T upstream_gene_variant 0.4
rrs 1471866 n.21C>T non_coding_transcript_exon_variant 0.29
rrs 1471869 n.24G>T non_coding_transcript_exon_variant 0.33
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.67
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.67
rrs 1471931 n.87delA non_coding_transcript_exon_variant 0.67
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.67
rrs 1471979 n.134T>C non_coding_transcript_exon_variant 0.71
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.71
rrs 1472019 n.174G>A non_coding_transcript_exon_variant 0.6
rrs 1472023 n.178G>T non_coding_transcript_exon_variant 0.6
rrs 1472029 n.184C>T non_coding_transcript_exon_variant 0.5
rrs 1472030 n.185G>T non_coding_transcript_exon_variant 0.5
rrs 1472033 n.188A>C non_coding_transcript_exon_variant 0.4
rrs 1472035 n.190G>T non_coding_transcript_exon_variant 0.4
rrs 1472040 n.195T>G non_coding_transcript_exon_variant 0.5
rrs 1472043 n.198T>G non_coding_transcript_exon_variant 0.57
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.57
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.57
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.57
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.57
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.43
rrs 1472324 n.479G>T non_coding_transcript_exon_variant 0.29
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.33
rrs 1472337 n.492C>G non_coding_transcript_exon_variant 0.33
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.29
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.5
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.5
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.4
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.33
rrs 1472624 n.779T>C non_coding_transcript_exon_variant 0.15
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.3
rrs 1472762 n.917C>T non_coding_transcript_exon_variant 0.2
rrs 1472811 n.966G>T non_coding_transcript_exon_variant 0.25
rrs 1472836 n.991G>T non_coding_transcript_exon_variant 0.2
rrs 1472841 n.996G>T non_coding_transcript_exon_variant 0.22
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 0.33
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.33
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.33
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.33
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.64
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.64
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.6
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.55
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.55
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.6
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.7
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.67
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.67
rrs 1473072 n.1227T>A non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.36
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.36
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.36
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.42
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.36
rrl 1473668 n.11C>T non_coding_transcript_exon_variant 0.22
rrl 1473697 n.40C>T non_coding_transcript_exon_variant 0.33
rrl 1473699 n.42A>G non_coding_transcript_exon_variant 0.33
rrl 1473717 n.60G>A non_coding_transcript_exon_variant 0.54
rrl 1473731 n.74T>A non_coding_transcript_exon_variant 0.5
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.56
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.6
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.62
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.69
rrl 1473814 n.157A>C non_coding_transcript_exon_variant 0.73
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.73
rrl 1473816 n.159C>G non_coding_transcript_exon_variant 0.73
rrl 1473828 n.171G>C non_coding_transcript_exon_variant 0.78
rrl 1473829 n.172G>C non_coding_transcript_exon_variant 0.7
rrl 1473830 n.173T>G non_coding_transcript_exon_variant 0.7
rrl 1473831 n.174G>T non_coding_transcript_exon_variant 0.7
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.5
rrl 1473887 n.230T>A non_coding_transcript_exon_variant 0.5
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.5
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.5
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.5
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.5
rrl 1473936 n.279A>G non_coding_transcript_exon_variant 0.5
rrl 1474199 n.542G>T non_coding_transcript_exon_variant 0.2
rrl 1474257 n.600G>T non_coding_transcript_exon_variant 0.29
rrl 1474412 n.755G>T non_coding_transcript_exon_variant 0.25
rrl 1474519 n.862G>T non_coding_transcript_exon_variant 0.25
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.5
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 1.0
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.75
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.6
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.33
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.33
rrl 1474917 n.1260G>T non_coding_transcript_exon_variant 1.0
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.5
rrl 1475343 n.1686A>G non_coding_transcript_exon_variant 0.67
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.57
rrl 1475358 n.1701T>C non_coding_transcript_exon_variant 0.67
rrl 1475363 n.1706C>T non_coding_transcript_exon_variant 0.67
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.8
rrl 1475380 n.1723C>A non_coding_transcript_exon_variant 0.8
rrl 1475381 n.1724G>T non_coding_transcript_exon_variant 0.8
rrl 1475382 n.1725A>C non_coding_transcript_exon_variant 0.8
rrl 1475395 n.1738T>G non_coding_transcript_exon_variant 0.8
rrl 1475396 n.1739C>G non_coding_transcript_exon_variant 0.8
rrl 1475397 n.1740G>T non_coding_transcript_exon_variant 0.8
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.8
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.8
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.8
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 1.0
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 1.0
rrl 1475647 n.1990G>C non_coding_transcript_exon_variant 0.2
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.2
rrl 1475692 n.2035G>T non_coding_transcript_exon_variant 0.17
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.42
rrl 1475759 n.2102C>T non_coding_transcript_exon_variant 0.45
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.45
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.45
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.45
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.45
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.45
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.29
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.29
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.33
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.22
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.22
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.25
rrl 1476248 n.2591G>T non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.33
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.38
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.25
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.33
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.33
rrl 1476308 n.2651G>T non_coding_transcript_exon_variant 0.22
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.29
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.4
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.44
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.5
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.5
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.38
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.25
rrl 1476679 n.3022T>C non_coding_transcript_exon_variant 0.25
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.29
rrl 1476778 n.3121G>A non_coding_transcript_exon_variant 0.25
fabG1 1674139 p.Gly234Arg missense_variant 0.12
inhA 1674165 c.-37C>A upstream_gene_variant 0.12
rpsA 1834096 c.555G>C synonymous_variant 0.12
rpsA 1834099 c.558C>G synonymous_variant 0.12
rpsA 1834102 c.561T>C synonymous_variant 0.12
rpsA 1834108 c.567C>G synonymous_variant 0.12
rpsA 1834135 c.594G>T synonymous_variant 0.17
rpsA 1834150 c.609G>C synonymous_variant 0.2
rpsA 1834165 c.624A>G synonymous_variant 0.2
rpsA 1834168 c.627C>T synonymous_variant 0.2
rpsA 1834169 p.Thr210Ala missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 0.2
rpsA 1834213 c.672G>C synonymous_variant 0.38
rpsA 1834231 c.690T>C synonymous_variant 0.2
rpsA 1834234 c.693G>C synonymous_variant 0.19
rpsA 1834240 c.699T>C synonymous_variant 0.17
rpsA 1834249 c.708T>C synonymous_variant 0.19
rpsA 1834261 c.720A>G synonymous_variant 0.17
rpsA 1834264 c.723G>C synonymous_variant 0.16
rpsA 1834279 c.738C>T synonymous_variant 0.14
rpsA 1834294 c.753G>C synonymous_variant 0.13
rpsA 1834299 p.Gln253Pro missense_variant 0.12
rpsA 1834303 c.762T>C synonymous_variant 0.12
rpsA 1834306 c.765T>C synonymous_variant 0.12
rpsA 1834471 p.Phe310Leu missense_variant 0.15
rpsA 1834721 p.Glu394Lys missense_variant 0.13
ndh 2101694 p.Ala450Asp missense_variant 0.13
ndh 2101800 p.Leu415Val missense_variant 0.15
ndh 2102514 p.Gly177Trp missense_variant 0.15
ndh 2102942 p.Lys34Arg missense_variant 0.17
PPE35 2170786 c.-174G>T upstream_gene_variant 0.15
Rv1979c 2222106 c.1059C>T synonymous_variant 0.18
Rv1979c 2222553 c.612G>A synonymous_variant 0.12
Rv1979c 2223088 p.Ser26* stop_gained 0.13
pncA 2289004 p.Asp80Tyr missense_variant 0.12
pncA 2289469 c.-228C>A upstream_gene_variant 0.17
kasA 2518045 c.-70G>T upstream_gene_variant 0.13
kasA 2518296 p.Gly61Val missense_variant 0.17
kasA 2519224 c.1110C>G synonymous_variant 0.11
kasA 2519227 c.1113G>C synonymous_variant 0.12
kasA 2519239 c.1125A>C synonymous_variant 0.13
kasA 2519248 c.1134C>T synonymous_variant 0.14
kasA 2519257 c.1143C>T synonymous_variant 0.15
kasA 2519260 c.1146T>C synonymous_variant 0.14
kasA 2519263 c.1149C>T synonymous_variant 0.15
kasA 2519266 c.1152C>T synonymous_variant 0.14
kasA 2519272 c.1158C>G synonymous_variant 0.14
kasA 2519275 c.1161C>A synonymous_variant 0.14
kasA 2519278 c.1164A>G synonymous_variant 0.14
kasA 2519281 c.1167G>T synonymous_variant 0.14
kasA 2519284 c.1170C>G synonymous_variant 0.16
kasA 2519287 c.1173T>C synonymous_variant 0.16
kasA 2519293 c.1179T>C synonymous_variant 0.16
kasA 2519298 p.Arg395Gln missense_variant 0.17
kasA 2519305 c.1191A>C synonymous_variant 0.14
kasA 2519306 p.Val398Ile missense_variant 0.14
kasA 2519323 c.1209G>C synonymous_variant 0.12
pepQ 2859464 p.Gly319Cys missense_variant 0.18
Rv2752c 3064944 c.1248G>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 0.14
Rv3083 3448627 p.Gly42Ser missense_variant 0.14
Rv3083 3448847 p.Arg115Leu missense_variant 0.17
whiB7 3568589 p.Asp31Tyr missense_variant 0.13
whiB7 3568661 p.Pro7Thr missense_variant 0.14
fbiA 3641120 p.Ser193Tyr missense_variant 0.15
rpoA 3877584 c.924C>G synonymous_variant 0.11
rpoA 3877587 c.921A>G synonymous_variant 0.1
rpoA 3878271 c.237T>C synonymous_variant 0.17
rpoA 3878360 p.Ala50Ser missense_variant 0.12
clpC1 4039397 c.1308A>G synonymous_variant 0.14
clpC1 4039409 c.1296T>C synonymous_variant 0.16
clpC1 4039412 c.1293T>G synonymous_variant 0.17
clpC1 4039415 p.Glu430Asp missense_variant 0.17
clpC1 4039430 c.1275T>C synonymous_variant 0.2
clpC1 4039442 c.1263A>G synonymous_variant 0.2
clpC1 4039448 c.1257A>G synonymous_variant 0.19
clpC1 4039454 c.1251A>T synonymous_variant 0.19
clpC1 4039463 c.1242C>G synonymous_variant 0.18
clpC1 4039466 c.1239T>C synonymous_variant 0.2
clpC1 4039469 c.1236T>C synonymous_variant 0.2
clpC1 4039472 c.1233G>C synonymous_variant 0.21
clpC1 4039481 c.1224T>C synonymous_variant 0.2
clpC1 4039484 c.1221T>C synonymous_variant 0.19
clpC1 4039487 c.1218G>C synonymous_variant 0.18
clpC1 4039517 c.1188C>G synonymous_variant 0.12
clpC1 4040057 c.648C>T synonymous_variant 0.12
panD 4043942 p.Pro114Thr missense_variant 0.13
embC 4240756 c.894G>C synonymous_variant 0.12
embC 4240774 c.912C>G synonymous_variant 0.11
embC 4240780 c.918T>C synonymous_variant 0.1
embC 4240783 c.921G>C synonymous_variant 0.11
embC 4240789 c.927T>C synonymous_variant 0.1
embA 4245173 c.1941G>T synonymous_variant 0.17
ethA 4326438 p.Leu346Met missense_variant 0.18
ethA 4327013 p.Ser154* stop_gained 0.15