TB-Profiler result

Run: SRR8692898
Summary

Run ID: SRR8692898

Sample name:

Date: 13-08-2023 20:05:05

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 0.84 linezolid
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 5620 c.381G>T synonymous_variant 0.13
gyrB 5863 c.624G>T synonymous_variant 0.18
gyrB 5990 p.Phe251Leu missense_variant 0.11
gyrB 6272 p.Leu345Ile missense_variant 0.12
gyrA 8927 p.Lys542Asn missense_variant 0.12
gyrA 9218 c.1917C>T synonymous_variant 0.18
gyrA 9230 c.1929T>C synonymous_variant 0.14
gyrA 9236 c.1935G>C synonymous_variant 0.13
gyrA 9242 c.1941A>C synonymous_variant 0.12
gyrA 9248 c.1947G>C synonymous_variant 0.12
gyrA 9252 p.Val651Ile missense_variant 0.12
gyrA 9266 p.Asp655Glu missense_variant 0.12
gyrA 9267 p.Asn656Gly missense_variant 0.12
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 0.12
gyrA 9304 p.Gly668Glu missense_variant 0.18
gyrA 9311 c.2010C>T synonymous_variant 0.12
gyrA 9326 c.2025G>C synonymous_variant 0.1
gyrA 9532 p.Gly744Val missense_variant 0.14
mshA 575211 c.-137G>T upstream_gene_variant 0.18
mshA 576093 p.Pro249Leu missense_variant 0.2
ccsA 620649 c.759A>G synonymous_variant 0.14
ccsA 620658 c.768C>A synonymous_variant 0.14
ccsA 620661 c.771C>G synonymous_variant 0.13
ccsA 620694 c.804C>G synonymous_variant 0.14
ccsA 620698 p.Val270Ile missense_variant 0.14
ccsA 620703 c.813G>C synonymous_variant 0.14
ccsA 620712 c.822G>C synonymous_variant 0.14
ccsA 620718 c.828G>C synonymous_variant 0.14
rpoC 762470 c.-900G>C upstream_gene_variant 0.1
rpoC 762488 c.-882G>C upstream_gene_variant 0.13
rpoC 762491 c.-879T>C upstream_gene_variant 0.13
rpoC 763940 p.Ala191Ser missense_variant 0.14
rpoC 763945 c.576T>C synonymous_variant 0.14
rpoC 763947 p.Ala193Val missense_variant 0.14
rpoC 763951 c.582G>C synonymous_variant 0.14
rpoC 763960 c.591T>G synonymous_variant 0.15
rpoC 763963 c.594C>T synonymous_variant 0.15
rpoC 763987 c.618C>T synonymous_variant 0.18
rpoC 763991 p.Ile208Leu missense_variant 0.17
rpoC 764005 c.636G>C synonymous_variant 0.17
rpoC 764024 c.655_657delTTGinsCTC synonymous_variant 0.2
rpoC 764029 p.Glu220Asp missense_variant 0.2
rpoC 764032 p.Asp221Glu missense_variant 0.2
rpoC 764209 c.840C>A synonymous_variant 0.22
rpoC 764530 c.1161C>T synonymous_variant 0.22
rpoC 764539 c.1170C>G synonymous_variant 0.22
rpoC 764548 c.1179G>T synonymous_variant 0.25
rpoC 764575 c.1206T>G synonymous_variant 0.22
rpoC 764611 c.1242G>T synonymous_variant 0.25
rpoC 764626 c.1257C>T synonymous_variant 0.25
rpoC 764632 c.1263T>C synonymous_variant 0.25
rpoC 764650 c.1281G>T synonymous_variant 0.23
rpoC 764662 c.1293G>C synonymous_variant 0.15
rpoC 764674 p.Gln435His missense_variant 0.13
rpoC 764677 c.1308C>G synonymous_variant 0.13
rpoC 764719 c.1350G>A synonymous_variant 0.14
rpoC 764746 c.1377G>T synonymous_variant 0.2
rpoC 764752 c.1383G>C synonymous_variant 0.24
rpoC 764758 c.1389C>G synonymous_variant 0.24
rpoC 764764 c.1395T>C synonymous_variant 0.24
rpoC 764800 c.1431G>A synonymous_variant 0.25
rpoC 764803 c.1434C>T synonymous_variant 0.25
rpoC 764809 c.1440C>T synonymous_variant 0.26
rpoC 764815 c.1446A>G synonymous_variant 0.28
rpoC 764827 c.1458G>C synonymous_variant 0.37
rpoC 764858 c.1489T>C synonymous_variant 0.23
rpoC 764869 c.1500C>T synonymous_variant 0.26
rpoC 764878 c.1509C>G synonymous_variant 0.25
rpoC 764887 c.1518G>C synonymous_variant 0.22
rpoC 764888 c.1519T>C synonymous_variant 0.22
rpoC 764912 p.Met515Leu missense_variant 0.1
rpoC 764948 c.1579T>C synonymous_variant 0.11
rpoC 765670 p.His767Gln missense_variant 0.18
rpoC 765784 c.2415C>T synonymous_variant 0.25
rpoC 766462 c.3093G>T synonymous_variant 0.29
rpoC 766738 c.3369G>T synonymous_variant 0.17
rpoC 766750 c.3381C>G synonymous_variant 0.17
rpoC 766765 c.3396A>C synonymous_variant 0.18
rpoC 766771 c.3402G>C synonymous_variant 0.17
rpoC 766774 c.3405T>C synonymous_variant 0.17
rpoC 766775 p.Arg1136Lys missense_variant 0.17
rpoC 766798 c.3429C>G synonymous_variant 0.15
rpoC 766804 c.3435A>G synonymous_variant 0.15
rpoC 766807 c.3438T>C synonymous_variant 0.14
rpoC 766837 c.3468G>C synonymous_variant 0.14
rpoC 766843 c.3474T>C synonymous_variant 0.15
rpoC 767023 p.Asp1218Glu missense_variant 0.29
rpoC 767119 c.3750A>G synonymous_variant 0.18
rpoC 767210 p.Ala1281Ser missense_variant 0.17
mmpL5 777143 p.Glu446Asp missense_variant 0.12
mmpL5 777951 p.Ala177Val missense_variant 0.22
mmpL5 778075 p.Ala136Thr missense_variant 0.22
mmpL5 778819 c.-339C>A upstream_gene_variant 0.14
mmpS5 778851 p.Ala19Ser missense_variant 0.14
mmpL5 779314 c.-834G>T upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.11
rpsL 781715 c.156T>C synonymous_variant 0.12
rpsL 781728 c.169T>C synonymous_variant 0.12
rpsL 781735 p.Ser59Thr missense_variant 0.12
rpsL 781738 p.Gln60Arg missense_variant 0.12
rpsL 781742 c.183C>T synonymous_variant 0.12
rpsL 781751 c.192G>C synonymous_variant 0.12
rpsL 781754 c.195G>C synonymous_variant 0.12
rpsL 781760 c.201T>C synonymous_variant 0.12
rpsL 781769 c.210G>A synonymous_variant 0.15
rpsL 781805 c.246G>C synonymous_variant 0.2
rpsL 781811 c.252C>T synonymous_variant 0.25
rpsL 781814 c.255C>T synonymous_variant 0.25
rpsL 781817 c.258G>T synonymous_variant 0.25
rpsL 781829 c.270G>C synonymous_variant 0.25
fbiC 1302761 c.-170G>T upstream_gene_variant 0.12
fbiC 1303480 p.Gln184Lys missense_variant 0.12
Rv1258c 1406302 c.1039C>A synonymous_variant 0.18
Rv1258c 1406317 p.Gln342Lys missense_variant 0.2
Rv1258c 1406466 p.Ser292* stop_gained 0.13
Rv1258c 1406686 p.Val219Ile missense_variant 1.0
Rv1258c 1407350 c.-10C>A upstream_gene_variant 0.2
embR 1416694 c.654C>A synonymous_variant 0.14
embR 1416810 c.536_537delAG frameshift_variant 0.12
atpE 1461165 c.121C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.6
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.6
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472355 n.510C>A non_coding_transcript_exon_variant 0.22
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.17
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.2
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.2
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.2
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.29
rrs 1472600 n.755C>A non_coding_transcript_exon_variant 0.2
rrs 1472784 n.939A>G non_coding_transcript_exon_variant 0.25
rrs 1473287 n.1442C>T non_coding_transcript_exon_variant 0.29
rrl 1474043 n.386G>T non_coding_transcript_exon_variant 0.33
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 0.25
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.29
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.29
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.29
rrl 1474498 n.841G>A non_coding_transcript_exon_variant 0.29
rrl 1474505 n.848C>T non_coding_transcript_exon_variant 0.29
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.29
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.29
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.29
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.22
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.6
rrl 1475343 n.1686A>G non_coding_transcript_exon_variant 0.8
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.8
rrl 1475358 n.1701T>C non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>T non_coding_transcript_exon_variant 1.0
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 1.0
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 0.71
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.67
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.5
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.4
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.5
rrl 1475759 n.2102C>T non_coding_transcript_exon_variant 0.5
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.5
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.5
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 0.53
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.16
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.16
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.17
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.12
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.12
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.13
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.13
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.13
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.13
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.13
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.13
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.2
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.38
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.4
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.5
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.5
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.5
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 0.75
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.75
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.75
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.4
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476707 n.3050C>A non_coding_transcript_exon_variant 0.5
fabG1 1673875 p.Gly146Cys missense_variant 0.14
inhA 1674251 p.Thr17Asn missense_variant 0.12
inhA 1674778 p.Pro193Ser missense_variant 0.14
rpsA 1833434 c.-108C>A upstream_gene_variant 0.14
rpsA 1833676 c.135A>G synonymous_variant 0.11
rpsA 1833679 c.138G>C synonymous_variant 0.12
rpsA 1833694 c.153G>T synonymous_variant 0.12
rpsA 1833697 c.156C>G synonymous_variant 0.12
rpsA 1834289 p.Glu250* stop_gained 0.14
tlyA 1918086 c.147C>T synonymous_variant 0.12
tlyA 1918506 c.567A>G synonymous_variant 0.11
ndh 2101761 p.Gln428Lys missense_variant 0.18
ndh 2102038 c.1005C>A synonymous_variant 0.12
ndh 2103140 c.-98G>T upstream_gene_variant 0.25
katG 2154610 p.Pro501Gln missense_variant 0.22
katG 2155354 p.Arg253Leu missense_variant 0.14
katG 2156359 c.-248C>A upstream_gene_variant 0.25
PPE35 2167698 p.Asn972Ile missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 0.15
PPE35 2168373 p.Pro747Gln missense_variant 0.18
PPE35 2168934 p.Ile560Thr missense_variant 0.17
Rv1979c 2221998 c.1167G>T synonymous_variant 0.14
Rv1979c 2222085 c.1080G>A synonymous_variant 0.15
Rv1979c 2222110 p.Ser352Tyr missense_variant 0.18
pncA 2289011 c.231C>A synonymous_variant 0.13
kasA 2517941 c.-174C>G upstream_gene_variant 0.14
kasA 2518688 p.Val192Ile missense_variant 0.18
kasA 2518702 c.588C>T synonymous_variant 0.18
kasA 2518711 c.597A>G synonymous_variant 0.2
kasA 2518714 c.600A>T synonymous_variant 0.2
kasA 2518715 p.Pro201Ala missense_variant 0.2
kasA 2518732 c.618C>G synonymous_variant 0.33
kasA 2518747 c.633C>G synonymous_variant 0.5
kasA 2518756 c.642G>T synonymous_variant 0.4
kasA 2518759 c.645C>G synonymous_variant 0.4
kasA 2518780 p.Glu222Asp missense_variant 0.4
kasA 2518783 c.669T>G synonymous_variant 0.4
kasA 2518787 p.Arg225Gly missense_variant 0.4
kasA 2518792 c.678C>G synonymous_variant 0.4
kasA 2518795 c.681C>G synonymous_variant 0.4
kasA 2518798 c.684G>T synonymous_variant 0.4
kasA 2518813 c.699C>T synonymous_variant 0.29
eis 2714639 p.Asp232Asn missense_variant 0.17
folC 2746794 p.Gln269Lys missense_variant 0.15
folC 2747747 c.-149C>A upstream_gene_variant 0.15
pepQ 2859453 c.966G>T synonymous_variant 0.18
pepQ 2860484 c.-66G>T upstream_gene_variant 0.2
ribD 2987238 p.Thr134Ala missense_variant 0.2
ribD 2987552 p.Met238Ile missense_variant 0.12
Rv2752c 3064674 c.1518C>A synonymous_variant 0.12
Rv2752c 3066310 c.-119G>T upstream_gene_variant 0.12
Rv2752c 3067163 c.-972C>T upstream_gene_variant 0.18
thyA 3074260 p.Trp71Leu missense_variant 0.17
thyA 3074340 c.132G>T synonymous_variant 0.17
ald 3086935 p.Ala39Asp missense_variant 0.22
fbiD 3339310 p.Asp65His missense_variant 0.11
whiB7 3568456 p.Ser75* stop_gained 0.14
Rv3236c 3612132 p.Ala329Ser missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 0.12
Rv3236c 3612970 p.Leu49Phe missense_variant 0.13
fbiA 3640933 p.Ala131Ser missense_variant 0.17
fbiB 3641295 c.-240G>T upstream_gene_variant 0.33
fbiB 3642246 p.Asn238Asp missense_variant 0.14
alr 3840893 c.528G>T synonymous_variant 0.17
alr 3841128 p.Leu98Pro missense_variant 0.12
alr 3841177 c.244C>T synonymous_variant 0.13
alr 3841588 c.-168C>A upstream_gene_variant 0.15
alr 3841593 c.-173C>A upstream_gene_variant 0.14
rpoA 3877928 p.Leu194Met missense_variant 0.22
rpoA 3878157 c.351C>G synonymous_variant 0.2
rpoA 3878160 c.348C>G synonymous_variant 0.2
rpoA 3878163 c.345C>T synonymous_variant 0.2
rpoA 3878184 c.324C>T synonymous_variant 0.22
rpoA 3878193 c.315T>C synonymous_variant 0.22
rpoA 3878197 p.Glu104Ala missense_variant 0.18
rpoA 3878205 c.303T>C synonymous_variant 0.17
rpoA 3878217 c.291A>G synonymous_variant 0.18
rpoA 3878244 c.264G>A synonymous_variant 0.2
rpoA 3878253 c.255G>C synonymous_variant 0.2
rpoA 3878256 c.252G>C synonymous_variant 0.2
rpoA 3878262 p.Ser82Gly missense_variant 0.2
rpoA 3878271 c.237T>C synonymous_variant 0.18
rpoA 3878283 p.Glu75Asp missense_variant 0.18
rpoA 3878292 c.216T>C synonymous_variant 0.2
clpC1 4039024 p.Glu561* stop_gained 0.15
clpC1 4039229 c.1476C>A synonymous_variant 0.12
clpC1 4039299 p.Arg469Leu missense_variant 0.15
clpC1 4040249 c.456A>G synonymous_variant 0.22
clpC1 4040411 c.294T>C synonymous_variant 0.13
clpC1 4040426 c.279T>C synonymous_variant 0.12
clpC1 4040431 c.274T>C synonymous_variant 0.11
clpC1 4040433 p.Ser91Thr missense_variant 0.11
clpC1 4040435 c.270G>C synonymous_variant 0.11
clpC1 4040450 c.255A>G synonymous_variant 0.11
clpC1 4040459 c.246C>G synonymous_variant 0.12
clpC1 4040462 c.243C>T synonymous_variant 0.12
clpC1 4040465 c.240T>C synonymous_variant 0.12
clpC1 4040471 c.234T>C synonymous_variant 0.11
clpC1 4040480 c.225T>C synonymous_variant 0.11
clpC1 4040522 c.183T>C synonymous_variant 0.14
clpC1 4040531 c.174T>C synonymous_variant 0.14
clpC1 4040537 c.168G>C synonymous_variant 0.18
clpC1 4040540 c.165G>C synonymous_variant 0.18
clpC1 4040551 c.154T>C synonymous_variant 0.15
clpC1 4040558 c.147G>C synonymous_variant 0.11
clpC1 4040561 c.144A>G synonymous_variant 0.11
clpC1 4040573 c.132T>C synonymous_variant 0.12
clpC1 4040579 c.126A>G synonymous_variant 0.12
clpC1 4040582 c.123G>C synonymous_variant 0.12
clpC1 4040585 c.120A>G synonymous_variant 0.12
clpC1 4040588 c.117T>C synonymous_variant 0.13
clpC1 4040594 c.111G>C synonymous_variant 0.13
clpC1 4040600 c.103_105delTTAinsCTC synonymous_variant 0.15
clpC1 4040603 c.102T>G synonymous_variant 0.15
clpC1 4040606 c.99T>C synonymous_variant 0.15
clpC1 4040644 c.61A>C synonymous_variant 0.13
clpC1 4040648 c.57G>A synonymous_variant 0.14
panD 4044145 p.Ile46Asn missense_variant 0.17
panD 4044171 c.111C>T synonymous_variant 0.2
panD 4044371 c.-90G>T upstream_gene_variant 0.22
embA 4243803 p.Ile191Val missense_variant 0.18
embA 4244876 c.1644G>T synonymous_variant 0.14
embB 4247503 p.Phe330Leu missense_variant 0.2
embB 4247845 c.1332G>T synonymous_variant 0.25
embB 4248726 p.Ser738Phe missense_variant 0.18
embB 4249034 p.Arg841Trp missense_variant 0.14
embB 4249380 p.Thr956Lys missense_variant 0.2
embB 4249616 p.Gly1035Cys missense_variant 0.15
aftB 4267102 p.Arg579Ser missense_variant 0.13
aftB 4268032 p.Pro269Thr missense_variant 0.2
aftB 4268504 c.333G>T synonymous_variant 0.18
aftB 4268556 p.Gly94Val missense_variant 0.13
ubiA 4269879 c.-46C>A upstream_gene_variant 0.12
ubiA 4269903 c.-70C>A upstream_gene_variant 0.17
ethA 4327262 p.Gly71Val missense_variant 0.14
ethR 4327693 p.Asp49Tyr missense_variant 0.2
ethA 4328019 c.-546G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 0.22
whiB6 4338709 c.-188G>T upstream_gene_variant 0.13
gid 4407535 p.Thr223Lys missense_variant 0.14
gid 4408110 c.93G>A synonymous_variant 0.17