TB-Profiler result

Run: ERR2514197
Summary

Run ID: ERR2514197

Sample name:

Date: 31-03-2023 20:10:48

Number of reads: 613757

Percentage reads mapped: 99.18

Strain: lineage1.1.1.1

Drug-resistance: RR-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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.98
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.99
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 761196 p.Leu464Met missense_variant 0.18 rifampicin
rpsA 1834962 p.Arg474Leu missense_variant 0.22 pyrazinamide
panD 4044220 p.His21Arg missense_variant 0.15 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6663 p.Phe475Ser missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7634 c.333C>T synonymous_variant 1.0
gyrA 7653 p.Ser118Thr missense_variant 0.13
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8622 p.Arg441Trp missense_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9602 c.2301T>A synonymous_variant 0.15
fgd1 490972 p.Arg64Ser missense_variant 1.0
fgd1 491240 p.Asp153Val missense_variant 0.2
fgd1 491247 p.Tyr155* stop_gained 0.13
fgd1 491406 p.Met208Ile missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575772 p.Val142Ala missense_variant 0.11
mshA 575782 c.435G>C synonymous_variant 0.11
mshA 575942 p.Arg199Cys missense_variant 0.2
mshA 576348 p.Thr334Lys missense_variant 0.17
ccsA 620016 c.126C>T synonymous_variant 0.15
ccsA 620392 p.Gln168Lys missense_variant 0.25
rpoB 761338 p.Arg511His missense_variant 0.13
rpoB 761915 c.2109C>T synonymous_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763924 p.Glu185Asp missense_variant 0.25
rpoC 764318 p.Val317Ile missense_variant 0.25
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765451 c.2082C>T synonymous_variant 0.18
rpoC 765692 p.Val775Leu missense_variant 0.25
rpoC 765826 c.2457T>C synonymous_variant 0.12
rpoC 765835 c.2466C>T synonymous_variant 0.12
rpoC 765850 c.2481G>C synonymous_variant 0.12
rpoC 765883 c.2514C>G synonymous_variant 0.22
rpoC 765886 c.2517C>G synonymous_variant 0.2
rpoC 765892 c.2523T>C synonymous_variant 0.2
rpoC 766393 c.3024C>A synonymous_variant 0.12
rpoC 766660 c.3291G>C synonymous_variant 0.17
rpoC 766672 c.3303T>C synonymous_variant 0.22
rpoC 766673 p.Gly1102Asn missense_variant 0.22
rpoC 766726 c.3357T>C synonymous_variant 0.17
rpoC 766738 c.3369G>C synonymous_variant 0.17
rpoC 766747 c.3378C>A synonymous_variant 0.12
rpoC 766765 c.3396A>C synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776199 p.Thr761Ile missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.23
mmpL5 777128 c.1353A>G synonymous_variant 0.17
mmpL5 777157 c.1324C>A synonymous_variant 0.14
mmpL5 777164 c.1317C>T synonymous_variant 0.12
mmpL5 777176 p.Glu435Asp missense_variant 0.12
mmpL5 777353 c.1128G>A synonymous_variant 1.0
mmpL5 777550 c.931C>T synonymous_variant 0.17
mmpL5 777551 c.930G>C synonymous_variant 0.2
mmpL5 777557 c.924T>C synonymous_variant 0.18
mmpL5 777581 p.Tyr300* stop_gained 1.0
mmpR5 778046 c.-944C>T upstream_gene_variant 0.25
mmpL5 778056 p.Ser142Thr missense_variant 0.27
mmpR5 778061 c.-929C>T upstream_gene_variant 0.12
mmpL5 778064 p.Ala139Ser missense_variant 0.12
mmpL5 778072 p.Thr137Ala missense_variant 0.12
mmpR5 778073 c.-917G>C upstream_gene_variant 0.12
mmpR5 778082 c.-908T>C upstream_gene_variant 0.15
mmpR5 778088 c.-902C>G upstream_gene_variant 0.18
mmpL5 778621 c.-141G>C upstream_gene_variant 0.14
mmpS5 779529 c.-624G>A upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781413 c.-147T>C upstream_gene_variant 0.14
rplC 800676 c.-133C>A upstream_gene_variant 0.14
fbiC 1303078 p.Ala50Thr missense_variant 0.17
fbiC 1304378 p.Leu483Pro missense_variant 0.14
fbiC 1305248 p.Ala773Val missense_variant 0.13
fbiC 1305264 c.2334C>T synonymous_variant 0.15
embR 1416562 c.786C>T synonymous_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472461 n.616G>T non_coding_transcript_exon_variant 0.14
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1475481 n.1824C>T non_coding_transcript_exon_variant 0.17
inhA 1674030 c.-172G>T upstream_gene_variant 0.18
inhA 1674465 c.264C>A synonymous_variant 0.25
rpsA 1833917 p.Val126Ile missense_variant 0.14
rpsA 1834319 p.Val260Ile missense_variant 1.0
rpsA 1834813 c.1272G>A synonymous_variant 0.14
rpsA 1834925 p.Gly462* stop_gained 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918635 c.696C>T synonymous_variant 0.22
ndh 2101796 p.Ser416* stop_gained 0.13
ndh 2101988 p.Ala352Val missense_variant 0.12
katG 2153936 p.Ala726Thr missense_variant 0.13
katG 2154280 p.Leu611Pro missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154744 c.1368C>A synonymous_variant 0.15
katG 2154788 p.Val442Ile missense_variant 0.13
katG 2154797 p.Gln439Lys missense_variant 0.12
katG 2155704 c.408C>A synonymous_variant 0.2
katG 2156389 c.-278G>C upstream_gene_variant 1.0
PPE35 2167763 p.Ile950Val missense_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.16
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.16
PPE35 2167965 p.Ala883Gly missense_variant 0.26
PPE35 2167967 c.2646A>C synonymous_variant 0.26
PPE35 2167983 p.Gly877Asp missense_variant 0.92
PPE35 2168182 p.Leu811Ile missense_variant 0.25
PPE35 2169054 p.Ala520Asp missense_variant 0.17
PPE35 2169680 c.932delG frameshift_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222618 p.Trp183Arg missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518535 p.Ala141Ser missense_variant 0.12
kasA 2518879 c.765A>G synonymous_variant 0.18
kasA 2518882 c.768C>A synonymous_variant 0.17
kasA 2519141 c.1027C>T synonymous_variant 0.18
kasA 2519169 p.Ala352Val missense_variant 0.17
ahpC 2726043 c.-150C>T upstream_gene_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.2
folC 2746244 p.Ala452Val missense_variant 0.13
folC 2746738 c.861C>T synonymous_variant 1.0
pepQ 2860116 c.303G>A synonymous_variant 0.17
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065237 p.Ser319Thr missense_variant 0.2
Rv2752c 3066362 c.-171G>T upstream_gene_variant 0.12
thyX 3067941 p.Ala2Asp missense_variant 0.14
thyA 3074207 p.Glu89* stop_gained 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.25
fbiD 3339366 c.249G>A synonymous_variant 0.13
fbiD 3339608 p.Pro164Leu missense_variant 0.33
Rv3083 3448485 c.-19C>G upstream_gene_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473942 c.-65C>T upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475048 p.Ile348Val missense_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3611992 c.1125T>C synonymous_variant 0.33
Rv3236c 3612198 p.Ala307Thr missense_variant 0.5
Rv3236c 3612465 p.Leu218Met missense_variant 0.14
fbiA 3641351 p.Ala270Asp missense_variant 0.17
fbiB 3641664 p.Asp44Tyr missense_variant 0.14
fbiB 3641726 c.192C>G synonymous_variant 0.18
fbiB 3642375 p.Ala281Thr missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3878530 c.-23C>T upstream_gene_variant 0.17
clpC1 4039039 p.Gly556Ser missense_variant 0.15
clpC1 4039042 p.Ser555Thr missense_variant 0.13
clpC1 4039243 c.1462C>T synonymous_variant 0.14
clpC1 4039645 p.His354Asp missense_variant 0.13
clpC1 4039654 p.Thr351Ser missense_variant 0.13
clpC1 4040057 c.648C>T synonymous_variant 0.2
clpC1 4040098 p.Val203Leu missense_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040867 c.-164delT upstream_gene_variant 0.13
panD 4044232 p.Cys17Ser missense_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240801 c.939C>T synonymous_variant 0.13
embC 4240803 p.Tyr314Phe missense_variant 0.13
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 0.4
embA 4243662 p.Asp144Asn missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245472 p.Ala747Val missense_variant 0.2
embA 4245849 p.Ala873Thr missense_variant 0.17
embA 4245969 p.Pro913Ser missense_variant 0.86
embB 4247298 p.Pro262Leu missense_variant 0.2
embB 4247554 c.1041T>C synonymous_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.17
aftB 4267336 p.Asp501Asn missense_variant 0.12
aftB 4267765 p.Pro358Thr missense_variant 0.18
aftB 4267839 p.Phe333Ser missense_variant 0.33
aftB 4268354 c.483G>A synonymous_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326656 p.Pro273Leu missense_variant 1.0
ethR 4326961 c.-588G>C upstream_gene_variant 0.23
ethR 4326964 c.-585G>A upstream_gene_variant 0.23
ethR 4326970 c.-579G>T upstream_gene_variant 0.2
ethR 4326982 c.-567C>G upstream_gene_variant 0.13
ethA 4327439 p.Ala12Asp missense_variant 0.17
ethR 4328005 p.Ile153Val missense_variant 1.0
ethA 4328439 c.-966C>T upstream_gene_variant 0.25
whiB6 4338242 p.Gln94Glu 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