TB-Profiler result

Run: ERR4821538
Summary

Run ID: ERR4821538

Sample name:

Date: 01-04-2023 17:18:36

Number of reads: 647823

Percentage reads mapped: 80.19

Strain: lineage3

Drug-resistance: Other

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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
lineage3 East-African-Indian CAS RD750 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.8 streptomycin
pncA 2289130 c.111delA frameshift_variant 0.12 pyrazinamide
ethA 4327294 p.Tyr60* stop_gained 0.12 ethionamide
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 5821 c.582G>T synonymous_variant 0.2
gyrB 6924 p.Phe562Ser missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9479 c.2179delA frameshift_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576301 c.954A>G synonymous_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778658 p.Gly83Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800925 c.119_120delGC frameshift_variant 0.13
rplC 801235 p.Ala143Thr missense_variant 0.15
fbiC 1303271 p.Leu114Pro missense_variant 0.14
fbiC 1303338 c.408C>A synonymous_variant 0.15
embR 1416412 c.936T>C synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471781 n.-65G>T upstream_gene_variant 0.15
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.27
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.5
rrs 1472386 n.543delT non_coding_transcript_exon_variant 0.29
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.46
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.5
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.68
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.77
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.8
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.8
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.8
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.8
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.73
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.57
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.81
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.83
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.83
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.78
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.21
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.2
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.21
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.14
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.18
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.17
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.18
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.23
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.21
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.21
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.54
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.73
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.68
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.81
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.8
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.8
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.77
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.74
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.4
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.3
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.35
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.21
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.2
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.38
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.22
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.44
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.29
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.29
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.22
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 0.22
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.25
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.27
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.15
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.17
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.14
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.33
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.12
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.19
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.25
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.25
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.27
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.27
rrl 1474345 n.688A>T non_coding_transcript_exon_variant 0.29
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.27
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.25
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.27
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.27
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.3
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.4
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.42
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.42
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.45
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.45
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.15
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.2
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.14
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.14
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.15
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.15
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.45
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.45
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.45
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.58
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.58
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.58
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.58
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.64
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
fabG1 1673984 p.Ala182Asp missense_variant 0.22
fabG1 1674059 p.Pro207Leu missense_variant 0.14
inhA 1674129 c.-73C>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918549 p.Arg204Cys missense_variant 0.12
ndh 2102973 p.Phe24Ile missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223210 c.-47delG upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289456 c.-215G>T upstream_gene_variant 0.15
eis 2714898 c.435C>A synonymous_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859428 p.Pro331Ser missense_variant 0.12
pepQ 2859549 c.870C>T synonymous_variant 0.12
pepQ 2860373 p.Ala16Ser missense_variant 0.17
ribD 2987562 p.His242Tyr missense_variant 0.15
Rv2752c 3065268 c.924A>G synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
ald 3087000 p.Ala61Ser missense_variant 0.22
Rv3083 3449870 p.Ser456Tyr missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474694 p.Leu230Met missense_variant 0.14
Rv3236c 3612218 p.Val300Ala missense_variant 0.11
fbiA 3640717 p.Cys59Arg missense_variant 0.15
fbiB 3641112 c.-423T>C upstream_gene_variant 0.11
fbiB 3642500 c.966C>A synonymous_variant 0.12
fbiB 3642655 p.Thr374Met missense_variant 0.12
fbiB 3642877 p.Lys448Arg missense_variant 1.0
clpC1 4038726 p.Thr660Asn missense_variant 0.12
clpC1 4039605 p.Glu367Val missense_variant 0.14
clpC1 4039805 c.900C>A synonymous_variant 0.13
clpC1 4040446 p.Val87Phe missense_variant 0.18
embC 4240272 c.413delC frameshift_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243945 p.Thr238Asn missense_variant 0.11
embA 4245214 p.Ala661Glu missense_variant 0.17
embA 4245651 p.Thr807Ala missense_variant 0.12
embB 4246568 p.Ala19Thr missense_variant 0.22
embB 4247420 p.Ile303Val missense_variant 0.12
embB 4247522 p.Leu337Met missense_variant 0.11
aftB 4266999 p.Cys613Ser missense_variant 0.17
aftB 4267105 p.Val578Leu missense_variant 0.12
aftB 4268802 p.Ala12Glu missense_variant 0.25
aftB 4269213 c.-377C>A upstream_gene_variant 0.14
ethA 4326698 p.Arg259Leu missense_variant 0.15
ethR 4326700 c.-849C>A upstream_gene_variant 0.15
ethR 4327657 p.Leu37Phe missense_variant 0.14
ethA 4327827 c.-354A>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0