TB-Profiler result

Run: ERR6336807
Summary

Run ID: ERR6336807

Sample name:

Date: 02-04-2023 02:04:07

Number of reads: 800707

Percentage reads mapped: 99.01

Strain: lineage1.2.1.2.1

Drug-resistance: HR-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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.99
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
katG 2155405 p.Asn236Thr missense_variant 0.12 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 0.13 pyrazinamide
embB 4247583 p.Ala357Val missense_variant 0.25 ethambutol
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 5407 c.168G>A synonymous_variant 0.12
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6850 c.-452C>T upstream_gene_variant 0.14
gyrB 7164 p.Ala642Gly missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8243 c.942C>T synonymous_variant 0.22
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8730 p.Gly477Arg missense_variant 0.12
gyrA 9120 p.Arg607Cys missense_variant 0.18
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
gyrA 9331 p.Asn677Ser missense_variant 0.14
fgd1 490691 c.-92G>A upstream_gene_variant 0.17
fgd1 490740 c.-42_-41delGC upstream_gene_variant 0.12
fgd1 490920 c.138C>T synonymous_variant 0.12
fgd1 491213 p.Ser144Asn missense_variant 0.17
fgd1 491443 p.Ser221Ala missense_variant 0.14
fgd1 491533 p.Pro251Ser missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491764 c.982C>T synonymous_variant 0.22
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575956 p.Glu203Asp missense_variant 0.33
mshA 576108 p.Ala254Gly missense_variant 0.43
mshA 576435 p.Gln363Pro missense_variant 0.25
mshA 576437 c.1091delC frameshift_variant 0.33
mshA 576470 p.Gly375Arg missense_variant 0.5
mshA 576782 p.Gly479Ser missense_variant 0.14
ccsA 619882 c.-9G>A upstream_gene_variant 0.12
ccsA 620760 c.870C>T synonymous_variant 0.12
ccsA 620828 p.Val313Gly missense_variant 0.15
rpoB 759735 c.-72G>A upstream_gene_variant 0.12
rpoB 760042 p.Gly79Asp missense_variant 0.12
rpoB 760353 p.Glu183Lys missense_variant 0.22
rpoB 760878 p.Pro358Ser missense_variant 0.5
rpoB 761151 p.Leu449Val missense_variant 0.5
rpoB 762246 c.2440C>T synonymous_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764201 p.Arg278Trp missense_variant 0.18
rpoC 764207 p.Val280Ile missense_variant 0.2
rpoC 764809 c.1440C>T synonymous_variant 1.0
rpoC 765004 c.1635G>C synonymous_variant 0.18
rpoC 765026 p.Ala553Thr missense_variant 0.22
rpoC 765103 c.1734G>A synonymous_variant 1.0
rpoC 765108 p.Asp580Gly missense_variant 0.5
rpoC 765114 c.1746delG frameshift_variant 0.33
rpoC 765486 p.Met706Lys missense_variant 0.13
rpoC 765777 p.Val803Gly missense_variant 0.13
rpoC 766027 c.2658G>A synonymous_variant 0.15
rpoC 766201 c.2832G>A synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775884 p.Ile866Thr missense_variant 0.2
mmpL5 775970 c.2511G>A synonymous_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776282 c.2199G>A synonymous_variant 0.17
mmpL5 776342 c.2139G>A synonymous_variant 0.2
mmpL5 776564 c.1917C>A synonymous_variant 0.2
mmpL5 776694 p.Val596Ser missense_variant 0.15
mmpL5 776702 c.1779C>T synonymous_variant 0.15
mmpL5 776726 c.1755C>T synonymous_variant 0.29
mmpL5 776732 c.1749C>T synonymous_variant 0.22
mmpL5 776735 c.1746C>T synonymous_variant 0.22
mmpL5 776738 c.1743C>T synonymous_variant 0.2
mmpL5 776741 c.1740C>G synonymous_variant 0.2
mmpL5 776744 c.1735_1737delCGCinsAGG synonymous_variant 0.17
mmpL5 777046 p.Ser479Pro missense_variant 1.0
mmpL5 777466 c.1015T>C synonymous_variant 0.22
mmpL5 778383 p.Val33Ala missense_variant 0.15
mmpR5 778405 c.-585T>G upstream_gene_variant 0.2
mmpL5 778891 c.-411C>T upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781913 c.354C>A synonymous_variant 0.2
rplC 800759 c.-50C>T upstream_gene_variant 0.15
rplC 800925 c.117C>T synonymous_variant 0.18
rplC 801195 c.387G>T synonymous_variant 0.22
rplC 801255 c.447C>G synonymous_variant 0.18
fbiC 1302821 c.-110G>A upstream_gene_variant 1.0
fbiC 1302936 c.6G>A synonymous_variant 0.14
fbiC 1303396 p.Arg156Cys missense_variant 0.33
fbiC 1303562 p.Met211Lys missense_variant 0.2
fbiC 1303658 p.Arg243His missense_variant 0.29
fbiC 1303788 p.His286Gln missense_variant 0.25
fbiC 1303851 c.921C>A synonymous_variant 0.29
fbiC 1303856 c.926_927insA frameshift_variant 0.4
fbiC 1303955 p.Glu342Val missense_variant 0.2
fbiC 1304618 p.Arg563Pro missense_variant 0.17
fbiC 1304624 p.Cys565Ser missense_variant 0.2
fbiC 1305003 c.2073C>T synonymous_variant 0.29
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406329 p.Thr338Ala missense_variant 0.2
Rv1258c 1406563 p.Leu260Val missense_variant 0.14
Rv1258c 1407465 c.-125G>A upstream_gene_variant 0.33
embR 1416377 p.Asn324Ser missense_variant 0.14
embR 1416532 c.816C>T synonymous_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417298 p.Gly17Glu missense_variant 0.12
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
atpE 1461036 c.-8delA upstream_gene_variant 0.14
atpE 1461054 p.Thr4Ser missense_variant 0.18
atpE 1461166 p.Arg41Pro missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473392 n.-266C>T upstream_gene_variant 0.2
rrl 1475510 n.1853A>C non_coding_transcript_exon_variant 0.4
rrl 1475721 n.2064C>T non_coding_transcript_exon_variant 0.33
fabG1 1673698 p.Ser87Pro missense_variant 0.25
fabG1 1674088 p.Val217Ile missense_variant 0.25
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674237 c.36T>C synonymous_variant 0.1
inhA 1674321 c.120G>A synonymous_variant 0.12
inhA 1674812 p.Gly204Ala missense_variant 0.13
inhA 1674966 c.765T>G synonymous_variant 0.2
rpsA 1833658 c.118delG frameshift_variant 0.12
rpsA 1833817 c.278delA frameshift_variant 0.33
rpsA 1834405 c.864C>T synonymous_variant 0.12
rpsA 1834421 p.Gly294Arg missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918187 p.Gly83Asp missense_variant 0.18
tlyA 1918294 p.Ala119Thr missense_variant 0.13
tlyA 1918745 c.806A>G stop_lost&splice_region_variant 0.33
ndh 2101766 p.Arg426His missense_variant 0.15
ndh 2101816 c.1227C>G synonymous_variant 0.11
ndh 2101950 p.Phe365Ile missense_variant 0.17
ndh 2102183 p.Arg287Lys missense_variant 0.15
ndh 2102296 c.747C>T synonymous_variant 0.22
ndh 2102358 p.Gly229Ser missense_variant 0.18
katG 2154296 p.Ala606Thr missense_variant 0.15
katG 2154298 p.Pro605Gln missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154845 p.Val423Leu missense_variant 0.14
katG 2155428 c.684C>T synonymous_variant 0.15
katG 2155916 p.Ala66Thr missense_variant 0.25
katG 2156446 c.-335C>T upstream_gene_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168470 p.Thr715Ala missense_variant 0.12
PPE35 2169488 c.1125G>A synonymous_variant 0.17
PPE35 2169551 c.1062C>T synonymous_variant 0.15
PPE35 2169969 p.Gly215Asp missense_variant 0.12
Rv1979c 2222167 p.Ser333Asn missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222486 p.Val227Ile missense_variant 0.15
Rv1979c 2222697 c.468C>T synonymous_variant 0.33
Rv1979c 2222758 p.Val136Glu missense_variant 0.18
Rv1979c 2223242 c.-78A>C upstream_gene_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288769 p.Asp158Val missense_variant 0.13
pncA 2288797 p.Asn149Asp missense_variant 0.14
pncA 2288934 p.Tyr103Ala missense_variant 0.13
pncA 2289116 c.126T>C synonymous_variant 0.14
pncA 2289215 c.27G>C synonymous_variant 0.12
pncA 2289561 c.-320T>C upstream_gene_variant 0.2
pncA 2289863 c.-622G>A upstream_gene_variant 0.18
pncA 2289901 c.-660G>A upstream_gene_variant 0.14
pncA 2289919 c.-678C>T upstream_gene_variant 0.18
pncA 2289988 c.-747G>A upstream_gene_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518792 c.678C>T synonymous_variant 0.15
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519146 c.1032C>T synonymous_variant 0.14
kasA 2519151 p.Ser346Leu missense_variant 0.12
kasA 2519267 p.Val385Ile missense_variant 0.12
eis 2714282 p.Met351Val missense_variant 0.13
eis 2714760 c.573A>T synonymous_variant 0.13
eis 2714934 c.399C>A synonymous_variant 0.25
eis 2714985 c.348G>A synonymous_variant 0.25
eis 2715338 c.-6G>A upstream_gene_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726211 p.Gly7Arg missense_variant 0.13
folC 2746926 c.672dupC frameshift_variant 0.17
folC 2747463 p.Ser46Gly missense_variant 0.25
folC 2747590 c.9G>A synonymous_variant 0.13
pepQ 2860436 c.-18C>T upstream_gene_variant 0.13
ribD 2986653 c.-186T>A upstream_gene_variant 0.22
ribD 2986820 c.-19A>T upstream_gene_variant 0.13
ribD 2987445 p.Val203Ile missense_variant 0.22
Rv2752c 3064548 p.Gln548His missense_variant 0.4
Rv2752c 3064692 c.1500T>C synonymous_variant 0.67
Rv2752c 3064763 p.Val477Ile missense_variant 0.13
Rv2752c 3065708 p.Ala162Pro missense_variant 0.11
Rv2752c 3065926 p.Ala89Gly missense_variant 0.13
Rv2752c 3066330 c.-139G>A upstream_gene_variant 0.18
thyX 3067297 p.Arg217Cys missense_variant 0.5
thyX 3067596 p.Val117Gly missense_variant 0.11
thyA 3073796 p.Pro226Ala missense_variant 0.22
thyA 3074113 p.Arg120His missense_variant 0.17
thyA 3074144 p.Asp110His missense_variant 0.12
thyA 3074386 p.Leu29Arg missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086975 c.156G>A synonymous_variant 0.15
ald 3087483 p.Ala222Thr missense_variant 0.25
ald 3087511 p.Arg231His missense_variant 0.17
ald 3087571 p.Ser251Leu missense_variant 0.25
fbiD 3339053 c.-65G>A upstream_gene_variant 0.18
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339547 p.Leu144Phe missense_variant 0.25
fbiD 3339661 p.Trp182Gly missense_variant 0.22
Rv3083 3448318 c.-186G>A upstream_gene_variant 0.4
Rv3083 3448692 c.189C>T synonymous_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448999 p.Pro166Ser missense_variant 0.25
Rv3083 3449184 c.681C>T synonymous_variant 0.29
Rv3083 3449203 c.701delT frameshift_variant 0.25
fprA 3473857 c.-150G>A upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474177 c.171C>T synonymous_variant 0.14
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474793 p.Gly263Arg missense_variant 0.25
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475230 c.1224C>T synonymous_variant 0.14
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612093 p.Gly342Arg missense_variant 0.17
Rv3236c 3612598 c.519G>A synonymous_variant 0.12
Rv3236c 3612668 p.Ala150Val missense_variant 0.25
Rv3236c 3613001 p.Ala39Val missense_variant 0.13
fbiA 3640484 c.-59T>C upstream_gene_variant 0.33
fbiA 3640513 c.-30G>C upstream_gene_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640718 p.Cys59Tyr missense_variant 0.2
fbiB 3640920 c.-615A>T upstream_gene_variant 0.13
fbiA 3641441 p.Gly300Glu missense_variant 0.22
fbiB 3641876 c.342C>T synonymous_variant 0.14
fbiB 3642286 p.Leu251Gln missense_variant 0.29
fbiB 3642473 p.Met313Ile missense_variant 0.5
alr 3840284 p.Trp379* stop_gained 0.29
alr 3840409 p.Val338Met missense_variant 0.17
alr 3840876 p.Ala182Val missense_variant 0.18
alr 3840899 c.522C>T synonymous_variant 0.14
alr 3840905 c.516C>T synonymous_variant 0.13
alr 3841261 p.Glu54Lys missense_variant 0.17
alr 3841365 p.Gly19Asp missense_variant 0.12
alr 3841368 c.52_53insT frameshift_variant 0.14
alr 3841372 p.Gly17Arg missense_variant 0.13
alr 3841378 p.Thr15Ala missense_variant 0.13
alr 3841398 p.Val8Asp missense_variant 0.12
alr 3841590 c.-170G>C upstream_gene_variant 0.15
rpoA 3877510 p.Glu333Gly missense_variant 0.2
rpoA 3877592 c.916C>T synonymous_variant 0.22
rpoA 3877868 p.Thr214Ala missense_variant 0.12
rpoA 3877957 p.Glu184Gly missense_variant 0.13
rpoA 3878081 p.Gly143Ser missense_variant 0.18
rpoA 3878316 c.192C>T synonymous_variant 0.18
rpoA 3878398 p.Ser37Trp missense_variant 0.25
ddn 3986906 p.Met21Ile missense_variant 0.17
ddn 3986940 p.Asp33Asn missense_variant 0.18
ddn 3986972 c.130_131delAT frameshift_variant 0.17
ddn 3986989 p.Leu49Gln missense_variant 0.17
clpC1 4038654 p.Gly684Asp missense_variant 0.22
clpC1 4038771 p.Gly645Val missense_variant 0.25
clpC1 4038841 p.Val622Met missense_variant 0.14
clpC1 4039071 p.Pro545Leu missense_variant 0.14
clpC1 4039104 p.Arg534Pro missense_variant 0.14
clpC1 4039108 p.Arg533Trp missense_variant 0.12
clpC1 4039601 c.1104G>A synonymous_variant 0.29
clpC1 4039813 p.Ala298Thr missense_variant 0.14
clpC1 4039934 c.771G>A synonymous_variant 0.17
clpC1 4040057 c.648C>T synonymous_variant 0.18
clpC1 4040430 p.Leu92Ser missense_variant 0.1
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040807 c.-103C>T upstream_gene_variant 0.18
panD 4043889 c.393G>T synonymous_variant 0.18
panD 4044337 c.-56G>A upstream_gene_variant 0.12
embC 4239962 p.Val34Met missense_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241279 p.Val473Met missense_variant 0.14
embC 4241691 p.Gly610Asp missense_variant 0.29
embC 4241725 c.1863G>A synonymous_variant 0.5
embC 4242181 c.2319G>A synonymous_variant 0.13
embC 4242323 p.Gly821Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242650 p.Arg930Cys missense_variant 0.15
embC 4242669 p.Ile936Thr missense_variant 0.18
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244105 c.873C>G synonymous_variant 0.25
embA 4244365 p.Gly378Asp missense_variant 0.15
embA 4244383 p.Leu384Pro missense_variant 0.2
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244773 p.Ser514Leu missense_variant 0.15
embA 4244953 p.Phe574Ser missense_variant 0.12
embA 4245069 p.Val613Met missense_variant 0.17
embA 4245141 p.Ile637Phe missense_variant 0.13
embA 4245183 c.1951C>T synonymous_variant 0.12
embA 4245741 p.Thr837Ala missense_variant 0.33
embA 4245808 p.Leu859Ser missense_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4246594 c.81C>T synonymous_variant 0.18
embB 4246807 c.294G>C synonymous_variant 0.13
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248147 p.Ile545Thr missense_variant 0.11
embB 4248319 c.1806A>T synonymous_variant 0.3
embB 4248421 c.1908G>T synonymous_variant 0.14
embB 4248510 p.Ile666Thr missense_variant 0.11
embB 4249190 c.2682delC frameshift_variant 0.2
embB 4249398 p.Ala962Val missense_variant 0.15
aftB 4267088 c.1749C>T synonymous_variant 0.17
aftB 4267132 p.Pro569Ser missense_variant 0.22
aftB 4267288 p.His517Asp missense_variant 0.18
aftB 4268240 p.Met199Ile missense_variant 0.15
aftB 4268480 c.357G>A synonymous_variant 0.25
aftB 4268493 p.Ala115Val missense_variant 0.14
aftB 4268568 p.Leu90Pro missense_variant 0.13
aftB 4268976 c.-140G>A upstream_gene_variant 0.17
aftB 4268997 c.-161G>A upstream_gene_variant 0.18
ubiA 4269152 p.Ala228Thr missense_variant 0.13
ubiA 4269283 p.Ser184Leu missense_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4269878 c.-45A>G upstream_gene_variant 0.15
ethA 4326188 p.Arg429Gln missense_variant 0.17
ethR 4326661 c.-888C>T upstream_gene_variant 0.33
ethA 4327354 p.Ser40Thr missense_variant 0.12
ethR 4327737 p.Phe63Leu missense_variant 0.17
ethR 4327921 p.Gln125* stop_gained 0.2
ethA 4328265 c.-792C>T upstream_gene_variant 0.25
ethA 4328269 c.-796C>T upstream_gene_variant 0.25
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
gid 4407915 c.288C>T synonymous_variant 0.18
gid 4408282 c.-80G>A upstream_gene_variant 0.15