TB-Profiler result

Run: SRR21277804
Summary

Run ID: SRR21277804

Sample name:

Date: 04-04-2023 01:44:22

Number of reads: 18210305

Percentage reads mapped: 97.97

Strain: lineage2.2.1

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
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
katG 2155733 p.Gln127* stop_gained 0.13 isoniazid
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8348 c.1047C>A synonymous_variant 0.9
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490683 c.-100C>A upstream_gene_variant 0.15
fgd1 490691 c.-92G>T upstream_gene_variant 0.15
fgd1 490694 c.-89G>T upstream_gene_variant 0.14
fgd1 491320 p.Ala180Ser missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 575393 p.Arg16Ser missense_variant 0.12
mshA 575700 p.Glu118Val missense_variant 0.1
mshA 575853 p.Trp169* stop_gained 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575915 p.Asp190Phe missense_variant 0.19
mshA 575930 p.Glu195* stop_gained 0.11
mshA 576235 c.888C>A synonymous_variant 0.12
mshA 576246 p.Gly300Val missense_variant 0.12
ccsA 619826 c.-65G>T upstream_gene_variant 0.22
ccsA 619990 p.Phe34Ile missense_variant 0.12
ccsA 619996 p.Phe36Ile missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761454 p.Glu550Lys missense_variant 0.11
rpoC 762680 c.-690C>A upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763957 p.Lys196Asn missense_variant 0.14
rpoC 763968 p.Gly200Val missense_variant 0.11
rpoC 764549 p.Pro394Thr missense_variant 0.11
rpoC 765324 p.Gly652Val missense_variant 0.13
rpoC 766064 p.Val899Ile missense_variant 0.22
rpoC 766144 c.2775G>T synonymous_variant 0.11
rpoC 766960 c.3591C>A synonymous_variant 0.14
rpoC 766967 p.Pro1200Thr missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801232 p.Gln142Lys missense_variant 0.12
rplC 801235 p.Ala143Thr missense_variant 0.1
fbiC 1303087 p.Asp53Asn missense_variant 0.15
fbiC 1303098 c.168C>A synonymous_variant 0.12
fbiC 1303128 c.198C>T synonymous_variant 0.12
fbiC 1303905 c.975G>A synonymous_variant 0.15
fbiC 1303906 p.Gly326Arg missense_variant 0.12
fbiC 1304268 c.1338G>T synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
Rv1258c 1407047 c.294C>G synonymous_variant 0.14
Rv1258c 1407103 p.Ala80Thr missense_variant 0.13
Rv1258c 1407217 p.Gly42Arg missense_variant 0.13
Rv1258c 1407508 c.-168G>T upstream_gene_variant 0.14
Rv1258c 1407515 c.-175G>T upstream_gene_variant 0.12
Rv1258c 1407516 c.-176G>T upstream_gene_variant 0.15
embR 1416959 p.Arg130Leu missense_variant 0.13
embR 1416961 p.Gly129Cys missense_variant 0.12
embR 1416974 p.Ala125Glu missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471743 n.-103T>A upstream_gene_variant 0.13
rpsA 1833355 c.-187C>T upstream_gene_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.93
tlyA 1918553 p.Ala205Glu missense_variant 0.1
tlyA 1918566 c.627C>A synonymous_variant 0.1
ndh 2101682 p.Gly454Val missense_variant 0.12
ndh 2101684 p.Gln453His missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155730 p.Arg128Trp missense_variant 0.12
katG 2155737 c.375C>T synonymous_variant 0.13
katG 2155764 p.His116Gln missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170102 p.Pro171Thr missense_variant 0.25
PPE35 2170344 p.Ala90Val missense_variant 0.11
PPE35 2170354 p.Ala87Ser missense_variant 0.14
PPE35 2170473 p.Ser47* stop_gained 0.12
PPE35 2170525 p.Ala30Thr missense_variant 0.19
PPE35 2170538 c.75G>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518596 p.Arg161Leu missense_variant 0.11
kasA 2518639 c.525G>T synonymous_variant 0.13
folC 2746299 p.Glu434* stop_gained 0.12
folC 2746302 p.Ala433Ser missense_variant 0.12
folC 2746358 p.Val414Asp missense_variant 0.25
folC 2746374 p.Pro409Thr missense_variant 0.17
folC 2746570 c.1029C>T synonymous_variant 0.11
folC 2746573 p.Met342Ile missense_variant 0.11
folC 2746644 p.Arg319Ser missense_variant 0.12
folC 2746841 p.Asp253Val missense_variant 0.1
folC 2747331 p.His90Tyr missense_variant 0.12
folC 2747789 c.-191G>A upstream_gene_variant 0.12
pepQ 2859592 p.Ala276Val missense_variant 0.12
pepQ 2859616 p.Ala268Asp missense_variant 0.12
pepQ 2859621 c.798G>A synonymous_variant 0.12
pepQ 2859624 c.795G>A synonymous_variant 0.11
pepQ 2859914 p.Glu169* stop_gained 0.16
pepQ 2859919 p.Arg167Leu missense_variant 0.14
pepQ 2859942 c.477C>A synonymous_variant 0.43
pepQ 2859947 p.Val158Met missense_variant 0.17
pepQ 2859962 p.Ala153Thr missense_variant 0.13
pepQ 2859964 p.Ala152Asp missense_variant 0.1
pepQ 2860222 p.Ser66* stop_gained 0.25
pepQ 2860226 p.Ala65Thr missense_variant 0.17
pepQ 2860589 c.-171G>T upstream_gene_variant 0.56
ribD 2986647 c.-192G>T upstream_gene_variant 0.17
ribD 2987387 c.549G>T synonymous_variant 0.12
ribD 2987495 c.657C>T synonymous_variant 0.14
Rv2752c 3066277 c.-86C>T upstream_gene_variant 0.1
Rv2752c 3067025 c.-834G>A upstream_gene_variant 0.18
thyX 3067851 p.Gly32Val missense_variant 0.11
thyX 3067856 c.90C>T synonymous_variant 0.12
thyA 3074536 c.-65G>A upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087327 p.Asp170Tyr missense_variant 0.11
fbiD 3339307 p.Pro64Thr missense_variant 0.14
fbiD 3339555 c.438C>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474927 c.921C>A synonymous_variant 0.13
fprA 3474983 p.Gly326Val missense_variant 0.15
fprA 3474999 c.993G>T synonymous_variant 0.12
fprA 3475004 p.Pro333Leu missense_variant 0.1
fprA 3475293 p.Phe429Leu missense_variant 0.11
Rv3236c 3612157 c.960G>A synonymous_variant 0.1
Rv3236c 3612170 p.Glu316Val missense_variant 0.14
Rv3236c 3612179 p.Ala313Asp missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 0.95
fbiB 3641628 p.Ala32Thr missense_variant 0.14
fbiB 3641640 p.Ala36Ser missense_variant 0.17
fbiB 3642391 p.Ala286Val missense_variant 0.13
fbiB 3642394 p.Pro287Leu missense_variant 0.14
fbiB 3642715 p.Gly394Val missense_variant 0.11
fbiB 3642797 p.Leu421Phe missense_variant 0.1
alr 3841029 p.Ala131Val missense_variant 0.17
alr 3841044 p.Ala126Gly missense_variant 0.25
alr 3841200 p.Ala74Asp missense_variant 0.11
rpoA 3878584 c.-77C>T upstream_gene_variant 0.11
clpC1 4039600 p.His369Asn missense_variant 0.1
clpC1 4040226 p.Gly160Val missense_variant 0.11
clpC1 4040228 c.477G>T synonymous_variant 0.11
clpC1 4040254 p.Ala151Thr missense_variant 0.12
panD 4044479 c.-198C>T upstream_gene_variant 0.11
embC 4240401 p.Pro180His missense_variant 0.12
embC 4240475 p.Ala205Ile missense_variant 0.11
embC 4240655 p.Ala265Ser missense_variant 0.18
embC 4241111 p.Val417Leu missense_variant 0.11
embC 4241676 p.Ala605Glu missense_variant 0.14
embC 4241680 c.1818C>A synonymous_variant 0.1
embC 4241689 c.1827G>A synonymous_variant 0.12
embC 4241691 p.Gly610Val missense_variant 0.12
embC 4242161 p.Ala767Thr missense_variant 0.12
embC 4242172 c.2310C>A synonymous_variant 0.14
embC 4242188 p.Ala776Ser missense_variant 0.1
embC 4242193 c.2331G>T synonymous_variant 0.11
embA 4242367 c.-866C>A upstream_gene_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242753 p.Arg964Leu missense_variant 0.14
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243616 c.384C>T synonymous_variant 0.11
embA 4243853 p.Met207Ile missense_variant 0.11
embA 4243959 p.Arg243Trp missense_variant 0.17
embA 4244204 p.Met324Ile missense_variant 0.11
embA 4244211 p.Pro327Thr missense_variant 0.21
embA 4244601 p.Ala457Ser missense_variant 0.14
embA 4244858 c.1626G>A synonymous_variant 0.2
embA 4244938 p.Lys569Met missense_variant 0.14
embA 4244948 c.1716G>T synonymous_variant 0.1
embA 4244949 p.Gln573* stop_gained 0.11
embB 4245665 c.-849C>A upstream_gene_variant 0.1
embA 4245820 p.Ser863Ile missense_variant 0.11
embB 4246019 c.-495G>A upstream_gene_variant 0.14
embA 4246035 p.Glu935* stop_gained 0.11
embB 4246793 p.Ala94Ser missense_variant 0.12
embB 4247018 p.Gly169Ser missense_variant 0.14
embB 4247298 p.Pro262Leu missense_variant 0.11
embB 4247647 p.Glu378Asp missense_variant 0.11
embB 4247802 p.Pro430Gln missense_variant 0.17
embB 4248585 p.Arg691Gln missense_variant 0.11
embB 4248591 p.Ala693Asp missense_variant 0.11
embB 4249264 c.2751G>T synonymous_variant 0.11
embB 4249354 c.2841G>T synonymous_variant 0.11
aftB 4267594 p.Ala415Ser missense_variant 0.11
aftB 4267631 c.1206C>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 0.91
aftB 4267676 c.1161G>A synonymous_variant 0.18
aftB 4268859 c.-23G>T upstream_gene_variant 0.12
aftB 4268867 c.-31G>T upstream_gene_variant 0.14
aftB 4268870 c.-34G>T upstream_gene_variant 0.2
aftB 4268876 c.-40G>A upstream_gene_variant 0.2
aftB 4268887 c.-51C>A upstream_gene_variant 0.1
ethA 4327599 c.-126G>T upstream_gene_variant 0.11
ethA 4328023 c.-550G>T upstream_gene_variant 0.13
ethR 4328032 p.Ala162Thr missense_variant 0.1
ethA 4328037 c.-564C>T upstream_gene_variant 0.18
ethR 4328041 p.Thr165Ser missense_variant 0.18
whiB6 4338246 p.Leu92Phe missense_variant 0.11
whiB6 4338341 p.Leu61Met missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407641 p.Val188Leu missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408324 c.-122C>A upstream_gene_variant 0.11