TB-Profiler result

Run: ERR6336759
Summary

Run ID: ERR6336759

Sample name:

Date: 02-04-2023 02:02:23

Number of reads: 1635318

Percentage reads mapped: 98.95

Strain: lineage1.2.1.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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
pncA 2288727 p.Leu172Pro 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
gyrB 5518 p.Ile93Met missense_variant 0.13
gyrB 5523 p.Thr95Ile missense_variant 0.13
gyrB 5538 p.Met100Thr missense_variant 0.1
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575337 c.-11T>C upstream_gene_variant 0.17
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575373 p.Gly9Asp missense_variant 0.12
mshA 575538 p.Asp64Gly missense_variant 0.12
mshA 575620 c.273G>T synonymous_variant 0.13
mshA 575621 p.Ala92Ser missense_variant 0.13
mshA 576506 p.Gly387Ser missense_variant 0.25
mshA 576781 c.1434G>A synonymous_variant 0.22
ccsA 619859 c.-32G>A upstream_gene_variant 0.15
ccsA 620122 p.Arg78Trp missense_variant 0.5
ccsA 620276 p.Leu129Pro missense_variant 0.15
ccsA 620301 c.411G>A synonymous_variant 0.14
rpoB 762697 p.Ala964Val missense_variant 0.15
rpoB 762702 p.Val966Met missense_variant 0.15
rpoB 762807 p.Lys1001Glu missense_variant 0.4
rpoC 762986 c.-384G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 0.97
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764532 p.Gly388Ala missense_variant 0.18
rpoC 764535 p.Arg389Gln missense_variant 0.22
rpoC 764649 p.Arg427Gln missense_variant 0.14
rpoC 765275 p.Arg636Trp missense_variant 0.14
rpoC 765548 p.Ser727Gly missense_variant 0.2
rpoC 765933 p.Gly855Val missense_variant 0.12
rpoC 765969 p.Thr867Ile missense_variant 0.15
rpoC 766162 c.2793C>T synonymous_variant 0.17
rpoC 766403 p.Met1012Leu missense_variant 0.12
rpoC 766527 p.Val1053Ala missense_variant 0.13
rpoC 766998 p.Ile1210Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777312 p.Pro390Leu missense_variant 0.22
mmpL5 777634 p.Gly283Ser missense_variant 0.25
mmpL5 777665 c.816G>A synonymous_variant 0.18
mmpL5 777961 p.Glu174Lys missense_variant 0.17
mmpR5 779380 p.Gln131* stop_gained 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303093 c.164delT frameshift_variant 0.17
fbiC 1303400 p.Gln157Arg missense_variant 0.12
fbiC 1303536 c.606G>A synonymous_variant 0.12
fbiC 1303564 p.Gly212Ser missense_variant 0.14
fbiC 1304439 p.Glu503Asp missense_variant 0.5
fbiC 1304817 p.His629Gln missense_variant 0.11
fbiC 1305216 c.2286C>T synonymous_variant 0.5
Rv1258c 1406262 p.Gly360Asp missense_variant 0.18
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406718 p.Leu208Trp missense_variant 0.11
Rv1258c 1406773 p.Ala190Thr missense_variant 0.14
Rv1258c 1407005 c.336G>A synonymous_variant 0.33
embR 1416408 p.His314Tyr missense_variant 0.13
embR 1416429 p.Ala307Thr missense_variant 0.15
embR 1416930 p.Ala140Thr missense_variant 0.13
embR 1416999 p.Ala117Thr missense_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
inhA 1673561 c.-641A>G upstream_gene_variant 0.15
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674813 c.612C>T synonymous_variant 0.18
rpsA 1833358 c.-184C>T upstream_gene_variant 1.0
rpsA 1834499 c.958C>T synonymous_variant 0.13
rpsA 1834562 p.Gly341Ser missense_variant 0.13
rpsA 1834865 p.Gly442Arg missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918158 c.219G>A synonymous_variant 0.13
tlyA 1918587 p.Gln216His missense_variant 0.29
tlyA 1918598 p.Trp220* stop_gained 0.4
ndh 2102006 p.Thr346Arg missense_variant 0.11
ndh 2102040 p.Gly335Ser missense_variant 0.12
ndh 2102266 c.777C>T synonymous_variant 0.13
ndh 2103188 c.-146T>A upstream_gene_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155296 p.Phe272Leu missense_variant 0.1
katG 2155744 p.Gly123Ala missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170491 p.Ala41Val missense_variant 0.17
PPE35 2170533 p.Ala27Val missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223330 c.-166C>A upstream_gene_variant 0.25
pncA 2288695 p.Val183Ile missense_variant 0.13
pncA 2289146 p.Ser32Arg missense_variant 0.25
pncA 2289462 c.-221C>T upstream_gene_variant 0.13
pncA 2289897 c.-656G>A upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518411 c.297C>G synonymous_variant 0.11
kasA 2518633 c.519G>C synonymous_variant 0.2
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519115 p.Ala334Val missense_variant 0.25
kasA 2519234 p.Glu374Lys missense_variant 0.18
eis 2714314 p.Cys340Tyr missense_variant 0.17
eis 2714967 c.366G>A synonymous_variant 0.18
eis 2715056 p.Arg93Trp missense_variant 0.17
eis 2715172 p.Pro54Leu missense_variant 0.18
eis 2715362 c.-30T>A upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726716 p.Ala175Val missense_variant 0.17
folC 2746275 p.Val442Ile missense_variant 0.17
folC 2746498 c.1101G>A synonymous_variant 0.12
folC 2746515 c.1084C>T synonymous_variant 0.13
folC 2746651 c.948T>C synonymous_variant 0.5
folC 2746678 c.921T>G synonymous_variant 0.12
folC 2746870 c.729G>A synonymous_variant 0.13
pepQ 2859781 p.Gln213Arg missense_variant 0.12
pepQ 2859785 p.Leu212Val missense_variant 0.17
pepQ 2860124 p.Ser99Cys missense_variant 0.4
pepQ 2860153 p.Glu89Val missense_variant 0.33
pepQ 2860157 p.Gly88Ser missense_variant 0.33
ribD 2987076 p.Val80Ile missense_variant 0.13
ribD 2987095 p.Gly86Asp missense_variant 0.18
ribD 2987457 p.Val207Met missense_variant 0.13
ribD 2987512 p.Arg225His missense_variant 0.2
Rv2752c 3066246 c.-55G>A upstream_gene_variant 0.12
Rv2752c 3066275 c.-84G>A upstream_gene_variant 0.22
Rv2752c 3066387 c.-197delC upstream_gene_variant 0.14
Rv2752c 3067144 c.-953G>C upstream_gene_variant 0.11
thyX 3067348 p.Ala200Thr missense_variant 0.25
thyX 3067372 p.Trp192Arg missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087818 p.Cys333Trp missense_variant 0.29
fbiD 3339023 c.-95G>C upstream_gene_variant 0.22
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448319 c.-185C>G upstream_gene_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448972 p.His157Tyr missense_variant 0.13
Rv3083 3449194 p.Gly231Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474040 p.Gly12Arg missense_variant 0.18
fprA 3474061 p.Ala19Thr missense_variant 0.18
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475044 c.1038C>T synonymous_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612020 p.Gly366Val missense_variant 0.12
Rv3236c 3612089 p.Leu343Pro missense_variant 0.14
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640820 p.Val93Gly missense_variant 0.14
fbiA 3641172 p.Met210Ile missense_variant 0.15
fbiA 3641533 p.Ala331Thr missense_variant 0.17
alr 3840484 p.Gly313Ser missense_variant 0.25
alr 3840623 c.798C>T synonymous_variant 0.17
alr 3840666 p.Arg252Gln missense_variant 0.18
rpoA 3877771 p.Ser246* stop_gained 0.11
rpoA 3878566 c.-59C>T upstream_gene_variant 0.18
rpoA 3878567 c.-60C>A upstream_gene_variant 0.18
ddn 3987041 c.198C>T synonymous_variant 0.17
clpC1 4038171 p.Pro845Arg missense_variant 0.22
clpC1 4039627 p.Lys360Glu missense_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239707 c.-156C>G upstream_gene_variant 0.12
embC 4240190 p.Pro110Ala missense_variant 0.13
embC 4240524 p.Arg221His missense_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241097 p.Ser412Leu missense_variant 0.2
embC 4241717 p.Arg619Trp missense_variant 0.67
embC 4242494 p.Asp878His missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242756 p.Ile965Asn missense_variant 0.18
embC 4243131 p.Pro1090Leu missense_variant 0.18
embA 4243407 p.Thr59Ala missense_variant 0.12
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244262 p.Leu344Met missense_variant 0.25
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244474 c.1242G>C synonymous_variant 0.2
embA 4244477 c.1245G>C synonymous_variant 0.29
embA 4244968 p.Gly579Val missense_variant 0.12
embA 4245420 c.2188C>T synonymous_variant 0.2
embA 4245507 p.Gly759Arg missense_variant 0.33
embB 4245584 c.-930C>T upstream_gene_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246336 p.Ala1035Val missense_variant 0.12
embA 4246471 p.Thr1080Ile missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.67
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54_55insT frameshift_variant 0.2
embB 4246588 c.75G>A synonymous_variant 0.22
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247705 p.Phe398Ile missense_variant 0.17
embB 4247924 p.Arg471Cys missense_variant 0.4
embB 4248324 p.Ala604Gly missense_variant 0.25
embB 4249222 c.2709C>T synonymous_variant 0.17
embB 4249397 p.Ala962Thr missense_variant 1.0
aftB 4266960 p.Arg626Gln missense_variant 0.13
aftB 4268246 c.591G>A synonymous_variant 0.2
aftB 4268344 p.Arg165Gly missense_variant 0.25
aftB 4268405 c.432G>A synonymous_variant 0.2
aftB 4268445 p.Ala131Val missense_variant 0.17
aftB 4268619 p.Val73Gly missense_variant 0.15
ubiA 4269223 p.Ala204Val missense_variant 0.12
aftB 4269225 c.-389C>G upstream_gene_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269591 c.-755C>T upstream_gene_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4328154 c.-681C>T upstream_gene_variant 0.14
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0