TB-Profiler result

Run: ERR6336796
Summary

Run ID: ERR6336796

Sample name:

Date: 02-04-2023 02:03:41

Number of reads: 662035

Percentage reads mapped: 98.95

Strain: lineage1.2.1.2

Drug-resistance: MDR-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 1.0
lineage1.2.1.2 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
rpoB 761248 p.Glu481Gly missense_variant 0.14 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.95 isoniazid, ethionamide
gid 4407796 p.Ser136* stop_gained 1.0 streptomycin
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6270 p.Asn344Thr missense_variant 0.2
gyrB 6273 p.Leu345Pro missense_variant 0.2
gyrB 6780 p.His514Pro missense_variant 0.11
gyrB 6927 c.1690delG frameshift_variant 0.17
gyrA 7084 c.-218A>G upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7698 c.397C>A synonymous_variant 0.17
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 575368 c.21T>C synonymous_variant 1.0
mshA 575387 p.Ala14Thr missense_variant 0.15
ccsA 619892 c.2T>A start_lost 0.12
ccsA 620607 c.717T>C synonymous_variant 0.18
ccsA 620697 c.807C>T synonymous_variant 0.18
ccsA 620701 p.Ala271Thr missense_variant 0.18
rpoC 762668 c.-702C>T upstream_gene_variant 0.22
rpoB 763001 p.Met1065Ile missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763358 c.-12A>G upstream_gene_variant 0.12
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 764093 p.Arg242Cys missense_variant 0.14
rpoC 764577 p.Ser403Phe missense_variant 0.2
rpoC 764972 p.Asp535Asn missense_variant 0.12
rpoC 765492 p.Val708Ala missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776036 c.2445G>C synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776574 p.Ala636Val missense_variant 0.18
mmpL5 777434 c.1047C>T synonymous_variant 0.12
mmpL5 777948 p.Pro178Arg missense_variant 0.2
mmpL5 778249 p.Ile78Val missense_variant 0.12
mmpL5 778351 p.Ala44Thr missense_variant 0.12
mmpL5 778946 c.-466A>T upstream_gene_variant 0.13
mmpR5 779326 p.Glu113Lys missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781905 p.Arg116Cys missense_variant 0.15
rpsL 781927 p.Lys123Thr missense_variant 0.14
rplC 801388 p.Ile194Val missense_variant 0.14
fbiC 1304508 p.Glu526Asp missense_variant 0.14
fbiC 1304513 p.Val528Gly missense_variant 0.13
fbiC 1305130 p.Gly734Cys missense_variant 0.18
fbiC 1305421 p.Ala831Ser missense_variant 0.12
Rv1258c 1406247 p.Leu365Ser missense_variant 0.12
Rv1258c 1406268 p.Ala358Val missense_variant 0.12
Rv1258c 1407467 c.-127C>A upstream_gene_variant 0.17
embR 1416329 p.Val340Asp missense_variant 0.14
embR 1416564 p.Ala262Thr missense_variant 0.14
embR 1416975 p.Ala125Ser missense_variant 0.14
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
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.91
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.13
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.13
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 1.0
inhA 1674162 c.-40C>T upstream_gene_variant 0.18
inhA 1674484 p.Ile95Leu missense_variant 0.81
rpsA 1834322 p.Glu261Lys missense_variant 0.43
rpsA 1834396 c.855G>A synonymous_variant 0.17
rpsA 1834553 p.Val338Ile missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918202 p.Asp88Gly missense_variant 0.12
ndh 2102277 p.Gly256Ser missense_variant 0.18
ndh 2103167 c.-125A>G upstream_gene_variant 0.29
katG 2154188 p.Pro642Ser missense_variant 0.14
katG 2154450 p.Lys554Asn missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169522 p.Ala364Val missense_variant 0.13
PPE35 2169594 p.Gly340Asp missense_variant 0.12
PPE35 2169951 p.Asn221Ser missense_variant 0.18
PPE35 2170070 c.543G>A synonymous_variant 0.2
Rv1979c 2221943 p.Arg408Gly missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222326 p.Asn280Ser missense_variant 0.18
Rv1979c 2223236 c.-72C>G upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288742 p.Thr167Ile missense_variant 0.15
pncA 2289411 c.-170G>A upstream_gene_variant 0.12
pncA 2289427 c.-186T>C upstream_gene_variant 0.12
kasA 2518011 c.-104G>A upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518229 p.Gly39Ser missense_variant 0.17
kasA 2518318 c.204C>T synonymous_variant 0.18
kasA 2518433 p.Arg107Trp missense_variant 0.14
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2715226 p.Trp36* stop_gained 0.12
ahpC 2725937 c.-256T>G upstream_gene_variant 0.14
ahpC 2725948 c.-245_-244insAA upstream_gene_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726259 c.67C>T synonymous_variant 0.12
folC 2746532 p.Pro356Leu missense_variant 0.29
folC 2747005 c.594C>T synonymous_variant 0.13
pepQ 2859407 p.Ile338Val missense_variant 0.12
pepQ 2859555 c.864G>A synonymous_variant 0.18
pepQ 2859568 p.Ala284Gly missense_variant 0.22
pepQ 2860598 c.-180C>T upstream_gene_variant 0.2
Rv2752c 3064751 p.Arg481Cys missense_variant 0.17
Rv2752c 3065161 p.Asn344Ile missense_variant 0.15
Rv2752c 3065389 p.Arg268His missense_variant 0.13
thyA 3074022 c.450C>T synonymous_variant 0.13
thyA 3074382 c.90C>T synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087005 c.186C>T synonymous_variant 0.12
ald 3087496 p.Glu226Val missense_variant 0.2
ald 3087606 p.Val263Ile missense_variant 0.14
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448889 p.Arg129Leu missense_variant 0.4
Rv3083 3449043 c.540C>T synonymous_variant 0.25
Rv3083 3449328 c.825C>T synonymous_variant 0.12
Rv3083 3449723 p.Cys407Tyr missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474939 c.933G>A synonymous_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3641104 p.Val188Phe missense_variant 0.79
alr 3840819 p.Asp201Gly missense_variant 0.17
rpoA 3877665 c.843C>T synonymous_variant 0.15
rpoA 3878567 c.-60C>G upstream_gene_variant 0.4
rpoA 3878642 c.-135G>A upstream_gene_variant 0.33
clpC1 4038238 p.Thr823Ala missense_variant 0.17
clpC1 4038833 c.1872C>T synonymous_variant 0.12
clpC1 4038845 c.1860G>A synonymous_variant 0.13
clpC1 4038876 p.Leu610Pro missense_variant 0.12
clpC1 4039300 p.Arg469Cys missense_variant 0.18
clpC1 4039613 c.1092C>T synonymous_variant 0.17
clpC1 4040147 p.Lys186Asn missense_variant 0.25
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240995 p.Ala378Glu missense_variant 0.18
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241113 c.1251G>A synonymous_variant 0.12
embC 4242518 p.Thr886Pro missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244415 p.Leu395Val missense_variant 0.18
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244465 c.1233C>T synonymous_variant 0.2
embA 4245052 c.1821delG frameshift_variant 0.18
embA 4245360 p.Val710Met missense_variant 0.17
embA 4245489 p.Val753Ile missense_variant 0.12
embA 4245550 p.Lys773Arg missense_variant 0.12
embB 4245587 c.-927G>A upstream_gene_variant 0.13
embA 4245621 p.Ala797Thr missense_variant 0.15
embA 4245643 p.Ala804Val missense_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246539 p.Lys9Arg missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4246548 p.Pro12Gln missense_variant 0.36
embB 4246555 c.42G>C synonymous_variant 0.31
embB 4246556 p.Ala15Pro missense_variant 0.31
embB 4246563 p.Leu17Trp missense_variant 0.21
embB 4246567 c.54G>T synonymous_variant 0.2
embB 4247098 c.585C>G synonymous_variant 0.18
embB 4247110 c.597G>T synonymous_variant 0.15
embB 4247368 c.855C>T synonymous_variant 0.12
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247598 c.1093_1095delCTG conservative_inframe_deletion 0.2
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247716 c.1203C>T synonymous_variant 0.15
embB 4248319 c.1806A>C synonymous_variant 0.2
embB 4248391 p.Met626Ile missense_variant 0.12
embB 4248755 p.Gly748Arg missense_variant 0.14
embB 4248780 p.Glu756Gly missense_variant 0.12
aftB 4267318 p.Gln507Glu missense_variant 0.13
aftB 4267791 p.Pro349Arg missense_variant 0.17
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 0.33
ethA 4327091 p.Ala128Val missense_variant 0.14
ethR 4327093 c.-456G>A upstream_gene_variant 0.13
ethA 4327495 c.-22A>G upstream_gene_variant 0.1
ethA 4328415 c.-942A>G upstream_gene_variant 0.17
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 4407902 p.Leu101Val missense_variant 0.1
gid 4408120 p.Gly28Val missense_variant 0.12