TB-Profiler result

Run: ERR5865353
Summary

Run ID: ERR5865353

Sample name:

Date: 01-04-2023 23:58:01

Number of reads: 469319

Percentage reads mapped: 99.57

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
ethA 4326770 c.703delT frameshift_variant 1.0 ethionamide, ethionamide
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 5471 p.Ala78Ser missense_variant 0.2
gyrB 5721 p.Gly161Val missense_variant 0.2
gyrA 7000 c.-302C>G upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7420 p.Ala40Glu missense_variant 0.15
gyrA 7425 p.Pro42Ser missense_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7736 c.435C>A synonymous_variant 0.43
gyrA 7739 p.Asp146Glu missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9464 c.2163C>A synonymous_variant 0.25
fgd1 491536 c.754C>T synonymous_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576056 p.Val237Met missense_variant 0.17
mshA 576557 p.His404Asn missense_variant 0.2
mshA 576577 c.1230C>A synonymous_variant 0.2
ccsA 619750 c.-141C>A upstream_gene_variant 0.22
ccsA 619893 c.3G>T start_lost 0.29
ccsA 619992 p.Phe34Leu missense_variant 0.25
ccsA 620503 p.Glu205* stop_gained 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759652 c.-155G>T upstream_gene_variant 0.21
rpoB 759772 c.-35C>A upstream_gene_variant 0.17
rpoB 759960 p.Thr52Ala missense_variant 0.12
rpoB 760178 c.372G>T synonymous_variant 0.17
rpoB 760254 p.Asp150Tyr missense_variant 0.2
rpoB 760628 p.Lys274Asn missense_variant 0.17
rpoB 761066 c.1260G>T synonymous_variant 0.18
rpoB 761351 c.1545C>T synonymous_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764224 p.Lys285Asn missense_variant 0.15
rpoC 764579 p.Asp404Tyr missense_variant 0.23
rpoC 764728 c.1361dupC frameshift_variant 0.11
rpoC 765461 p.Asn698His missense_variant 1.0
rpoC 765750 p.Pro794His missense_variant 0.2
rpoC 766202 p.Gly945Cys missense_variant 0.25
rpoC 766346 p.Glu993* stop_gained 0.18
rpoC 766393 c.3024C>A synonymous_variant 0.17
rpoC 766411 c.3042C>A synonymous_variant 0.18
rpoC 766414 p.Phe1015Leu missense_variant 0.2
rpoC 766475 p.Glu1036* stop_gained 0.25
rpoC 766489 c.3120G>A synonymous_variant 0.25
rpoC 766874 p.Asp1169Tyr missense_variant 0.2
rpoC 767088 p.Cys1240Phe missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775709 p.Phe924Leu missense_variant 0.25
mmpL5 776025 p.Ser819* stop_gained 0.25
mmpL5 776082 p.Ala800Val missense_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776235 p.Thr749Lys missense_variant 0.2
mmpL5 776270 p.Lys737Asn missense_variant 0.2
mmpL5 776458 p.Ala675Ser missense_variant 0.2
mmpL5 776477 c.2004G>T synonymous_variant 0.2
mmpL5 776528 p.Gln651His missense_variant 0.18
mmpL5 776945 p.Glu512Asp missense_variant 0.2
mmpL5 776981 c.1500G>T synonymous_variant 0.18
mmpL5 777004 p.Glu493* stop_gained 0.22
mmpL5 777152 p.Met443Ile missense_variant 0.25
mmpL5 777155 c.1326G>T synonymous_variant 0.22
mmpL5 777406 p.Ala359Ser missense_variant 0.18
mmpL5 778939 c.-459C>A upstream_gene_variant 0.29
mmpL5 778957 c.-477C>A upstream_gene_variant 0.25
mmpL5 779400 c.-920C>A upstream_gene_variant 0.17
mmpS5 779489 c.-584C>A upstream_gene_variant 0.2
mmpS5 779498 c.-593G>T upstream_gene_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781379 c.-181G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781446 c.-114G>T upstream_gene_variant 0.2
rpsL 781449 c.-111G>T upstream_gene_variant 0.2
rpsL 781451 c.-109G>T upstream_gene_variant 0.18
rpsL 781590 p.Gly11Cys missense_variant 0.29
rpsL 781692 p.Pro45Thr missense_variant 0.14
rplC 801308 p.Ala167Asp missense_variant 0.17
fbiC 1303371 c.441C>A synonymous_variant 0.29
fbiC 1304197 p.Gly423Cys missense_variant 0.18
fbiC 1304286 c.1356G>T synonymous_variant 0.2
fbiC 1304374 p.Glu482* stop_gained 0.25
fbiC 1304831 p.Ser634Tyr missense_variant 0.2
fbiC 1304881 p.Glu651* stop_gained 0.2
Rv1258c 1406404 p.Val313Phe missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406891 c.450C>T synonymous_variant 0.18
Rv1258c 1407216 p.Gly42Val missense_variant 0.15
embR 1416494 p.Gly285Val missense_variant 0.15
embR 1416672 p.Gly226Arg missense_variant 0.22
embR 1416795 p.Gly185Trp missense_variant 0.22
atpE 1461020 c.-25C>A upstream_gene_variant 0.17
atpE 1461029 c.-16C>A upstream_gene_variant 0.18
atpE 1461051 p.Pro3Thr missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473933 n.276C>A non_coding_transcript_exon_variant 0.33
rrl 1474702 n.1045G>T non_coding_transcript_exon_variant 0.4
rrl 1474785 n.1128T>C non_coding_transcript_exon_variant 0.33
rrl 1475316 n.1659G>T non_coding_transcript_exon_variant 0.5
rrl 1476304 n.2647G>A non_coding_transcript_exon_variant 0.22
rrl 1476569 n.2912G>T non_coding_transcript_exon_variant 0.25
fabG1 1673271 c.-169G>T upstream_gene_variant 0.18
fabG1 1673647 p.Arg70Cys missense_variant 0.22
fabG1 1673668 p.Glu77* stop_gained 0.18
inhA 1674414 c.213G>A synonymous_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917823 c.-117C>T upstream_gene_variant 0.15
tlyA 1917851 c.-89C>A upstream_gene_variant 0.18
tlyA 1917921 c.-19G>T upstream_gene_variant 0.25
tlyA 1917939 c.-1C>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918540 p.Pro201Thr missense_variant 0.18
ndh 2102417 p.Ala209Val missense_variant 1.0
katG 2154279 c.1833C>A synonymous_variant 0.25
katG 2154610 p.Pro501Gln missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154975 p.Ala379Ser missense_variant 0.18
katG 2155448 p.Ala222Ser missense_variant 0.25
katG 2156570 c.-459C>A upstream_gene_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168213 c.2400G>T synonymous_variant 0.29
PPE35 2168276 c.2337C>A synonymous_variant 0.18
PPE35 2168491 p.Ala708Ser missense_variant 0.17
PPE35 2168526 p.Gly696Val missense_variant 0.2
PPE35 2169233 p.Leu460Phe missense_variant 0.21
PPE35 2170363 p.Glu84* stop_gained 0.23
PPE35 2170445 c.168G>T synonymous_variant 0.17
PPE35 2170623 c.-11G>T upstream_gene_variant 0.15
PPE35 2170673 c.-61C>A upstream_gene_variant 0.25
Rv1979c 2222167 p.Ser333Ile missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223336 c.-172G>T upstream_gene_variant 0.3
pncA 2289635 c.-394G>T upstream_gene_variant 0.17
kasA 2518301 p.His63Asn missense_variant 0.22
kasA 2518580 p.Leu156Met missense_variant 0.18
kasA 2518750 p.Met212Ile missense_variant 0.33
kasA 2518778 p.Glu222* stop_gained 0.22
kasA 2518817 p.Asp235Tyr missense_variant 0.2
kasA 2519076 p.Ala321Glu missense_variant 0.25
kasA 2519151 p.Ser346* stop_gained 0.22
eis 2714167 p.Ala389Val missense_variant 0.15
eis 2714349 c.984G>T synonymous_variant 0.33
eis 2714942 p.Tyr131His missense_variant 0.12
eis 2715126 p.Leu69Phe missense_variant 0.25
eis 2715156 c.177C>A synonymous_variant 0.4
eis 2715395 c.-63C>T upstream_gene_variant 0.22
folC 2746272 p.Ala443Ser missense_variant 0.25
folC 2746312 c.1287G>T synonymous_variant 0.17
folC 2746683 p.Leu306Ile missense_variant 0.18
folC 2746835 p.Ser255* stop_gained 0.22
folC 2746968 p.Gly211Trp missense_variant 0.25
folC 2747200 c.399G>T synonymous_variant 0.25
pepQ 2859482 p.Ala313Thr missense_variant 0.4
pepQ 2860487 c.-69G>T upstream_gene_variant 0.22
ribD 2986658 c.-180delG upstream_gene_variant 0.2
ribD 2986693 c.-146C>A upstream_gene_variant 0.22
ribD 2987230 p.Ala131Glu missense_variant 0.17
Rv2752c 3064520 p.Val558Leu missense_variant 0.17
Rv2752c 3064580 p.Gly538Cys missense_variant 0.15
Rv2752c 3065008 p.Pro395Gln missense_variant 0.18
Rv2752c 3065121 p.Lys357Asn missense_variant 0.2
Rv2752c 3065507 p.Ala229Thr missense_variant 0.18
Rv2752c 3065534 p.Pro220Thr missense_variant 0.2
Rv2752c 3065871 p.Phe107Leu missense_variant 0.14
thyX 3068065 c.-120G>T upstream_gene_variant 0.15
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086928 p.Ala37Ser missense_variant 0.18
ald 3087170 p.Tyr117* stop_gained 0.15
ald 3087668 c.849C>T synonymous_variant 0.25
fbiD 3339412 p.Ala99Ser missense_variant 0.18
fbiD 3339438 c.321C>A synonymous_variant 0.17
fbiD 3339476 p.Leu120* stop_gained 0.18
fbiD 3339624 c.507G>A synonymous_variant 0.22
fbiD 3339732 c.615C>T synonymous_variant 0.18
Rv3083 3448534 p.Gly11Cys missense_variant 0.22
Rv3083 3448798 p.His99Asn missense_variant 0.18
Rv3083 3448823 p.Ala107Asp missense_variant 0.27
Rv3083 3449005 p.His168Asn missense_variant 0.18
Rv3083 3449331 c.828C>A synonymous_variant 0.29
fprA 3473809 c.-198G>T upstream_gene_variant 0.2
fprA 3473854 c.-153G>T upstream_gene_variant 0.17
fprA 3473874 c.-133C>A upstream_gene_variant 0.2
fprA 3473953 c.-54C>A upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474424 p.Gln140* stop_gained 0.33
fprA 3474476 p.Asn157Thr missense_variant 0.29
whiB7 3568786 c.-107C>A upstream_gene_variant 0.19
whiB7 3568834 c.-155G>T upstream_gene_variant 0.17
Rv3236c 3612118 c.999G>C synonymous_variant 0.18
Rv3236c 3612167 p.Gly317Val missense_variant 0.22
Rv3236c 3612495 c.622C>A synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613012 c.105G>T synonymous_variant 0.15
Rv3236c 3613068 p.Val17Leu missense_variant 0.17
fbiA 3640354 c.-189C>T upstream_gene_variant 0.15
fbiB 3640584 c.-951C>A upstream_gene_variant 0.22
fbiA 3641513 p.Cys324Phe missense_variant 0.17
fbiB 3641564 c.30G>T synonymous_variant 0.2
fbiB 3641963 c.429C>A synonymous_variant 0.29
alr 3840320 c.1101G>T synonymous_variant 0.2
alr 3840577 p.Ala282Ser missense_variant 0.2
alr 3840602 c.819G>T synonymous_variant 0.18
alr 3841132 p.Ala97Ser missense_variant 0.2
alr 3841465 c.-45G>T upstream_gene_variant 0.22
alr 3841466 c.-46A>G upstream_gene_variant 0.25
alr 3841619 c.-199G>T upstream_gene_variant 0.15
rpoA 3877490 p.Asp340Tyr missense_variant 0.17
rpoA 3877499 p.Asp337Tyr missense_variant 0.2
rpoA 3877533 c.975C>A synonymous_variant 0.2
rpoA 3878030 p.Gly160Trp missense_variant 0.27
rpoA 3878532 c.-25G>T upstream_gene_variant 0.4
ddn 3986646 c.-198C>A upstream_gene_variant 0.18
clpC1 4038629 c.2076G>T synonymous_variant 0.18
clpC1 4038779 c.1926C>T synonymous_variant 0.25
clpC1 4038946 p.Asp587Tyr missense_variant 1.0
clpC1 4038951 p.Phe585Ser missense_variant 1.0
clpC1 4038988 p.Asp573Tyr missense_variant 0.4
clpC1 4040183 p.Phe174Leu missense_variant 0.2
clpC1 4040212 p.Pro165Thr missense_variant 0.18
clpC1 4040317 p.Glu130* stop_gained 0.2
clpC1 4040374 p.Gly111Cys missense_variant 0.25
panD 4043995 p.Ala96Asp missense_variant 0.2
panD 4044003 p.Met93Ile missense_variant 0.17
panD 4044125 p.Ala53Ser missense_variant 0.15
embC 4239921 p.Arg20Leu missense_variant 0.22
embC 4240287 p.Ala142Asp missense_variant 0.17
embC 4240582 c.720C>A synonymous_variant 0.29
embC 4240792 p.Met310Ile missense_variant 0.2
embC 4240932 p.Trp357Leu missense_variant 0.33
embC 4241491 c.1629G>T synonymous_variant 0.17
embC 4241707 c.1845G>T synonymous_variant 0.15
embC 4242155 p.Met765Val missense_variant 0.11
embA 4242313 c.-920C>A upstream_gene_variant 0.3
embA 4242637 c.-596C>A upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243292 c.60G>T synonymous_variant 0.22
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244135 p.Glu301Asp missense_variant 0.2
embA 4244243 c.1011G>T synonymous_variant 0.2
embA 4244325 p.Gly365Cys missense_variant 0.22
embA 4244405 c.1173C>A synonymous_variant 0.25
embA 4244426 c.1194G>T synonymous_variant 0.17
embA 4244571 c.1339C>A synonymous_variant 0.2
embA 4244789 c.1557C>T synonymous_variant 0.2
embA 4245320 c.2088C>A synonymous_variant 0.33
embA 4245921 p.Gly897Cys missense_variant 0.17
embA 4245939 p.Gly903Cys missense_variant 0.17
embB 4246466 c.-48G>T upstream_gene_variant 0.18
embB 4246646 p.Pro45Thr missense_variant 0.18
embB 4247183 p.Gly224Arg missense_variant 0.25
embB 4247893 c.1380C>T synonymous_variant 0.17
embB 4247896 c.1383G>T synonymous_variant 0.25
embB 4248039 p.Arg509Leu missense_variant 0.15
embB 4248076 p.Glu521Asp missense_variant 0.18
embB 4248091 p.Tyr526* stop_gained 0.22
embB 4248598 c.2085A>G synonymous_variant 0.12
aftB 4267127 c.1710G>T synonymous_variant 0.2
aftB 4267551 p.Tyr429Cys missense_variant 0.15
aftB 4267574 c.1263G>T synonymous_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268881 c.-45C>A upstream_gene_variant 0.18
aftB 4269699 c.-863C>A upstream_gene_variant 0.15
ethA 4326033 p.Ala481Ser missense_variant 0.15
ethA 4327323 p.Pro51Thr missense_variant 0.2
ethA 4327458 p.Asp6Asn missense_variant 0.25
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408200 c.3G>T start_lost 0.15
gid 4408218 c.-16G>T upstream_gene_variant 0.14