TB-Profiler result

Run: SRR11972259
Summary

Run ID: SRR11972259

Sample name:

Date: 03-04-2023 05:33:57

Number of reads: 881381

Percentage reads mapped: 98.96

Strain: lineage1.2.1.2.1

Drug-resistance: Sensitive

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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 0.99
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.98
lineage1.2.1.2 Indo-Oceanic NA RD239 0.96
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.96
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
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
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 8701 p.Asp467Ala missense_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 0.92
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 575382 p.Leu12Ser missense_variant 0.14
mshA 575536 c.189T>C synonymous_variant 0.12
mshA 575619 p.Arg91Leu missense_variant 0.14
ccsA 619720 c.-171C>A upstream_gene_variant 0.2
ccsA 620073 c.183T>C synonymous_variant 0.22
ccsA 620262 c.372C>A synonymous_variant 0.14
rpoB 759638 c.-169_-168insA upstream_gene_variant 1.0
rpoB 760350 p.Asp182Tyr missense_variant 0.12
rpoB 760964 c.1158C>A synonymous_variant 0.12
rpoB 760987 p.Val394Ala missense_variant 0.12
rpoB 761210 c.1406_1407delTG frameshift_variant 0.33
rpoB 761281 p.Gly492Asp missense_variant 0.25
rpoB 761427 p.Pro541Thr missense_variant 0.19
rpoB 761672 c.1866C>T synonymous_variant 0.15
rpoB 762156 p.Val784Met missense_variant 0.12
rpoB 762249 p.Leu815Val missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763165 p.Lys1120Arg missense_variant 0.11
rpoC 763333 c.-37G>A upstream_gene_variant 0.18
rpoC 763401 p.Arg11Leu missense_variant 0.12
rpoC 763531 c.162G>C synonymous_variant 0.96
rpoC 763584 p.Gly72Val missense_variant 0.13
rpoC 763884 p.Ala172Val missense_variant 0.96
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763909 c.540C>T synonymous_variant 0.12
rpoC 765230 p.Ala621Thr missense_variant 0.22
rpoC 765490 c.2121C>A synonymous_variant 0.13
rpoC 765733 c.2364G>A synonymous_variant 0.15
rpoC 766020 p.Val884Gly missense_variant 0.22
rpoC 766543 c.3174C>A synonymous_variant 0.4
rpoC 766962 p.Gly1198Asp missense_variant 0.13
rpoC 766994 p.Gly1209Arg missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775657 p.Val942Phe missense_variant 0.23
mmpL5 775947 c.2483_2533delGTATCGAGCTGCACTGGTTGGTGTTGGCGATGGCGGTCATCATCCTGCTGG disruptive_inframe_deletion 0.22
mmpL5 776048 c.2433G>A synonymous_variant 0.18
mmpL5 776077 p.Ala802Ser missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777251 c.1230C>T synonymous_variant 0.18
mmpL5 777578 c.903C>A synonymous_variant 0.22
mmpL5 777631 p.Arg284Cys missense_variant 0.17
mmpR5 779192 p.Ser68Asn missense_variant 0.12
mmpR5 779384 p.Arg132Pro missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781677 p.Thr40Ser missense_variant 0.25
rpsL 781881 p.Lys108Glu missense_variant 0.11
rplC 801217 p.Ala137Ser missense_variant 0.14
rplC 801240 c.432G>A synonymous_variant 0.14
fbiC 1303612 p.Leu228Ile missense_variant 0.13
fbiC 1303873 c.944delT frameshift_variant 0.17
fbiC 1304346 p.Asp472Glu missense_variant 0.22
fbiC 1304419 p.Ala497Thr missense_variant 0.2
fbiC 1304507 p.Glu526Val missense_variant 0.17
fbiC 1304961 c.2031C>T synonymous_variant 0.17
Rv1258c 1406161 p.Ala394Thr missense_variant 0.2
Rv1258c 1406170 p.Gly391Trp missense_variant 0.2
Rv1258c 1406312 c.1029T>C synonymous_variant 0.91
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 1472695 n.850C>A non_coding_transcript_exon_variant 0.12
rrs 1472696 n.851G>A non_coding_transcript_exon_variant 0.12
fabG1 1673968 p.Thr177Ala missense_variant 0.13
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674417 c.216C>T synonymous_variant 0.18
inhA 1674926 p.Val242Ala missense_variant 0.18
rpsA 1833528 c.-14A>G upstream_gene_variant 0.11
rpsA 1834169 c.630delC frameshift_variant 0.13
rpsA 1834237 c.696C>T synonymous_variant 0.13
tlyA 1917922 c.-18A>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918535 p.His199Pro missense_variant 0.11
tlyA 1918688 p.Ala250Glu missense_variant 0.22
tlyA 1918743 c.804G>A synonymous_variant 0.12
ndh 2102465 p.Ala193Val missense_variant 0.23
katG 2154619 p.Arg498His missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155513 p.Lys200Arg missense_variant 0.12
katG 2155982 p.Asn44Asp missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167967 c.2646A>G synonymous_variant 0.97
PPE35 2170024 c.547_588delGCGGCCGTGGTGACCGCGCTCACCACGGCCGTGGGCATGCCG conservative_inframe_deletion 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289524 c.-283C>T upstream_gene_variant 1.0
pncA 2289864 c.-623A>G upstream_gene_variant 0.11
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518995 p.Ser294* stop_gained 0.22
kasA 2519048 p.Gly312Ser missense_variant 0.83
kasA 2519262 p.Asp383Val missense_variant 0.12
eis 2714217 c.1116T>C synonymous_variant 0.13
eis 2714970 c.363C>T synonymous_variant 0.14
eis 2715488 c.-156C>A upstream_gene_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746758 p.Gly281Arg missense_variant 0.22
pepQ 2859498 c.921C>A synonymous_variant 0.12
pepQ 2859681 p.Gln246His missense_variant 0.13
pepQ 2859843 c.576G>T synonymous_variant 0.22
pepQ 2859942 c.477C>A synonymous_variant 0.14
pepQ 2860193 p.Glu76Gln missense_variant 0.11
ribD 2987555 c.717C>A synonymous_variant 0.2
Rv2752c 3064619 p.Asp525Asn missense_variant 0.13
thyA 3073998 c.474G>A synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087460 p.Arg214Gln missense_variant 0.14
ald 3087879 c.1060C>A synonymous_variant 0.13
fbiD 3339008 c.-110A>G upstream_gene_variant 0.11
fbiD 3339329 p.Ala71Val missense_variant 0.12
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449589 c.1086C>A synonymous_variant 0.12
Rv3083 3449609 p.Glu369Val missense_variant 0.12
Rv3083 3449679 c.1176C>T synonymous_variant 0.12
fprA 3473981 c.-26G>T upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474477 p.Asn157Lys missense_variant 0.18
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474604 p.Arg200* stop_gained 0.22
fprA 3474877 p.Arg291Cys missense_variant 0.17
fprA 3475022 p.Gly339Val missense_variant 0.15
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 0.83
whiB7 3568830 c.-151T>A upstream_gene_variant 0.12
Rv3236c 3612450 c.667C>T synonymous_variant 0.13
Rv3236c 3612451 c.666G>A synonymous_variant 0.13
Rv3236c 3612618 p.Pro167Thr missense_variant 0.15
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640792 p.Glu84* stop_gained 0.18
fbiA 3640930 p.Glu130Gln missense_variant 0.15
fbiB 3641943 p.Arg137Cys missense_variant 0.18
fbiB 3642135 p.Ala201Thr missense_variant 0.17
fbiB 3642277 p.Ala248Val missense_variant 0.2
fbiB 3642420 c.886C>A synonymous_variant 0.13
fbiB 3642425 p.Phe297Leu missense_variant 0.13
fbiB 3642707 c.1176delG frameshift_variant 0.12
alr 3840657 p.Ile255Ser missense_variant 0.13
alr 3840662 c.759G>C synonymous_variant 0.13
ddn 3986912 c.69G>T synonymous_variant 0.12
clpC1 4038892 p.Glu605Gln missense_variant 0.18
clpC1 4039179 p.Arg509Gln missense_variant 0.15
clpC1 4039405 p.Glu434* stop_gained 0.12
clpC1 4039498 p.Ile403Val missense_variant 0.12
clpC1 4039508 c.1197G>C synonymous_variant 0.14
clpC1 4040448 p.Lys86Thr missense_variant 0.12
clpC1 4040457 c.247delC frameshift_variant 0.12
clpC1 4040495 c.210C>T synonymous_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239841 c.-22G>A upstream_gene_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241723 p.Val621Met missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243002 p.Ser1047Asn missense_variant 0.15
embC 4243070 p.Ala1070Ser missense_variant 0.14
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245571 p.Asp780Gly missense_variant 0.11
embB 4245857 c.-657C>A upstream_gene_variant 0.13
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.73
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246642 c.129G>T synonymous_variant 0.17
embB 4246787 p.Pro92Thr missense_variant 0.12
embB 4247099 p.Ala196Pro missense_variant 0.17
embB 4247578 c.1065G>A synonymous_variant 0.9
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249100 p.Tyr863His missense_variant 0.17
embB 4249109 p.Pro866Thr missense_variant 0.2
aftB 4267026 p.Arg604His missense_variant 0.14
aftB 4267056 p.Ser594Tyr missense_variant 0.14
aftB 4267268 c.1569T>C synonymous_variant 0.12
aftB 4267621 p.Gly406Cys missense_variant 0.29
aftB 4267670 c.1167G>A synonymous_variant 0.25
aftB 4267907 c.930C>T synonymous_variant 0.5
aftB 4267991 c.846G>C synonymous_variant 0.14
aftB 4268485 p.Leu118Phe missense_variant 0.25
aftB 4268493 p.Ala115Val missense_variant 0.25
aftB 4268630 c.207G>C synonymous_variant 0.12
ubiA 4269026 p.Leu270Met missense_variant 0.18
ubiA 4269046 p.Ala263Gly missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269586 p.Glu83Gly missense_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269633 c.-797G>T upstream_gene_variant 0.2
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4269888 c.-55C>G upstream_gene_variant 0.17
ethA 4326705 p.Pro257Ser missense_variant 0.12
ethR 4326901 c.-648C>T upstream_gene_variant 0.17
ethA 4327314 p.Arg54Cys missense_variant 0.12
whiB6 4338361 p.Arg54Gln missense_variant 0.93
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 4407657 c.546C>T synonymous_variant 0.17
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408106 c.97C>A synonymous_variant 0.14
gid 4408281 c.-79C>T upstream_gene_variant 0.17
PPE35 2170024 c.546_588delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA frameshift_variant 1.0