TB-Profiler result

Run: ERR2652925
Summary

Run ID: ERR2652925

Sample name:

Date: 31-03-2023 22:24:10

Number of reads: 417855

Percentage reads mapped: 95.64

Strain: lineage4.9

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 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 1472307 n.462C>T non_coding_transcript_exon_variant 0.17 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
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 7954 p.Ala218Glu missense_variant 0.4
gyrA 8465 c.1164C>A synonymous_variant 0.13
fgd1 490992 c.210G>T synonymous_variant 0.2
fgd1 491176 p.Leu132Met missense_variant 0.88
fgd1 491353 p.Gly191Ser missense_variant 0.15
fgd1 491441 p.Arg220Gln missense_variant 0.22
mshA 576506 p.Gly387Cys missense_variant 0.17
mshA 576758 p.His471Asp missense_variant 0.12
ccsA 620604 c.714C>T synonymous_variant 0.22
rpoB 760670 c.864G>C synonymous_variant 0.22
rpoB 760674 c.868T>C synonymous_variant 0.2
rpoB 760679 c.873A>G synonymous_variant 0.2
rpoB 760683 c.877T>C synonymous_variant 0.18
rpoB 760715 c.909C>G synonymous_variant 0.14
rpoB 760718 c.912C>T synonymous_variant 0.14
rpoB 760724 c.918T>C synonymous_variant 0.15
rpoB 760730 c.924T>C synonymous_variant 0.15
rpoB 760751 c.945G>C synonymous_variant 0.18
rpoB 760757 c.951T>C synonymous_variant 0.18
rpoB 760869 p.Val355Ile missense_variant 0.22
rpoB 760886 c.1080A>G synonymous_variant 0.25
rpoB 760925 c.1119T>C synonymous_variant 0.17
rpoB 760928 c.1122G>C synonymous_variant 0.17
rpoB 760931 c.1125C>G synonymous_variant 0.17
rpoB 760934 c.1128C>T synonymous_variant 0.17
rpoB 760946 c.1140A>G synonymous_variant 0.15
rpoB 760982 c.1176G>C synonymous_variant 0.14
rpoB 760985 c.1179G>C synonymous_variant 0.14
rpoB 760991 c.1185G>C synonymous_variant 0.14
rpoB 761279 c.1473C>T synonymous_variant 0.17
rpoB 761392 p.Glu529Gly missense_variant 0.12
rpoB 761732 c.1926C>T synonymous_variant 0.13
rpoC 762434 c.-936T>C upstream_gene_variant 0.15
rpoC 762449 c.-921C>A upstream_gene_variant 0.14
rpoC 762467 c.-903C>T upstream_gene_variant 0.12
rpoC 762488 c.-882G>C upstream_gene_variant 0.12
rpoB 762489 p.Val895His missense_variant 0.12
rpoC 762509 c.-861T>G upstream_gene_variant 0.12
rpoB 762510 p.Ala902Pro missense_variant 0.12
rpoC 762521 c.-849C>T upstream_gene_variant 0.13
rpoC 762533 c.-837T>C upstream_gene_variant 0.15
rpoC 762536 c.-834T>C upstream_gene_variant 0.17
rpoC 762537 c.-833T>C upstream_gene_variant 0.17
rpoC 762551 c.-819C>G upstream_gene_variant 0.2
rpoC 762929 c.-441G>C upstream_gene_variant 0.15
rpoC 762989 c.-381G>C upstream_gene_variant 0.15
rpoC 762995 c.-375G>T upstream_gene_variant 0.15
rpoC 763013 c.-357C>G upstream_gene_variant 0.13
rpoB 763291 p.Arg1162Leu missense_variant 0.15
rpoC 763554 p.Cys62Phe missense_variant 0.2
rpoC 764007 p.Gln213Arg missense_variant 0.15
rpoC 764365 c.996C>T synonymous_variant 0.17
rpoC 764968 c.1599T>C synonymous_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 0.17
rpoC 765613 p.His748Gln missense_variant 0.15
rpoC 765625 c.2256C>G synonymous_variant 0.15
rpoC 765631 p.Asp754Glu missense_variant 0.15
rpoC 765700 c.2331T>C synonymous_variant 0.14
rpoC 765775 c.2406C>T synonymous_variant 0.22
rpoC 766809 p.Val1147Ala missense_variant 0.18
mmpL5 776020 c.2461C>T synonymous_variant 0.17
mmpL5 776512 p.Ser657Thr missense_variant 0.12
mmpL5 776796 c.1684delG frameshift_variant 0.12
mmpR5 779275 p.Arg96Trp missense_variant 0.12
fbiC 1303200 c.270G>A synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471789 n.-57T>C upstream_gene_variant 0.18
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.17
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.17
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.17
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.17
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rpsA 1833590 p.Gly17Ser missense_variant 0.12
rpsA 1833940 c.399C>G synonymous_variant 0.14
rpsA 1833971 c.430C>T synonymous_variant 0.12
rpsA 1834021 c.480C>T synonymous_variant 0.13
rpsA 1834030 c.489C>G synonymous_variant 0.13
rpsA 1834570 p.Asp343Glu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169355 p.Gly420Ser missense_variant 0.2
PPE35 2169496 p.Asp373Asn missense_variant 0.5
pncA 2289027 p.Cys72Phe missense_variant 0.17
kasA 2518451 p.Gly113Cys missense_variant 0.17
eis 2714271 c.1062C>T synonymous_variant 0.17
ahpC 2726276 c.84C>T synonymous_variant 0.18
pepQ 2859994 p.Leu142Pro missense_variant 0.14
ribD 2987190 p.Ala118Thr missense_variant 0.17
Rv2752c 3064554 c.1638C>T synonymous_variant 0.14
Rv2752c 3064993 c.1198delT frameshift_variant 0.12
Rv2752c 3065437 c.754delG frameshift_variant 0.15
Rv2752c 3066334 c.-143T>C upstream_gene_variant 0.14
thyX 3067490 c.456C>G synonymous_variant 0.17
thyX 3067493 c.453A>G synonymous_variant 0.17
thyX 3067510 c.436C>T synonymous_variant 0.25
thyX 3067515 p.Ser144Thr missense_variant 0.31
thyX 3067530 p.Ala139Ser missense_variant 0.33
thyX 3067545 p.Glu134Ala missense_variant 0.33
thyX 3067549 p.Thr133Ala missense_variant 0.33
thyX 3067556 p.His130Gln missense_variant 0.31
thyX 3067559 c.387C>G synonymous_variant 0.31
thyX 3067565 p.Asp127Glu missense_variant 0.31
thyX 3067570 p.Ala126Pro missense_variant 0.31
thyX 3067577 c.369G>A synonymous_variant 0.31
thyX 3067601 p.Arg115His missense_variant 0.23
thyX 3067611 p.Lys112Thr missense_variant 0.21
thyX 3067619 c.327A>C synonymous_variant 0.27
thyX 3067631 c.315C>G synonymous_variant 0.27
thyX 3067634 c.312C>G synonymous_variant 0.21
thyX 3067652 c.294T>C synonymous_variant 0.17
thyX 3068018 c.-73G>T upstream_gene_variant 0.14
thyA 3073839 c.633T>C synonymous_variant 0.33
thyA 3073860 c.612C>G synonymous_variant 0.33
thyA 3073863 c.609T>C synonymous_variant 0.33
thyA 3073866 c.606C>G synonymous_variant 0.33
thyA 3073872 p.Ile200Val missense_variant 0.33
thyA 3073892 c.580T>C synonymous_variant 0.27
thyA 3073898 p.Ala192Ser missense_variant 0.27
thyA 3073917 c.555C>G synonymous_variant 0.27
thyA 3073920 c.552C>G synonymous_variant 0.27
thyA 3073925 c.547T>C synonymous_variant 0.3
thyA 3073929 c.543T>C synonymous_variant 0.3
thyA 3073941 c.531C>T synonymous_variant 0.25
thyA 3073953 c.519T>C synonymous_variant 0.18
thyA 3073956 c.516G>C synonymous_variant 0.18
thyA 3073959 c.513T>C synonymous_variant 0.17
thyA 3073977 c.495A>G synonymous_variant 0.18
thyA 3074004 c.468T>C synonymous_variant 0.18
thyA 3074010 c.462C>G synonymous_variant 0.25
thyA 3074028 c.444G>C synonymous_variant 0.18
thyA 3074031 c.441T>C synonymous_variant 0.2
thyA 3074037 c.435C>G synonymous_variant 0.25
thyA 3074053 p.Arg140Gln missense_variant 0.25
thyA 3074055 p.Glu139Pro missense_variant 0.25
thyA 3074061 c.411A>G synonymous_variant 0.22
thyA 3074079 c.393G>C synonymous_variant 0.22
thyA 3074097 c.375C>G synonymous_variant 0.29
thyA 3074100 p.Asp124Asn missense_variant 0.29
thyA 3074106 c.366T>C synonymous_variant 0.29
thyA 3074127 c.345G>C synonymous_variant 0.22
thyA 3074130 c.342G>C synonymous_variant 0.25
thyA 3074466 c.6G>A synonymous_variant 0.25
fbiD 3339300 c.183T>C synonymous_variant 0.29
Rv3083 3448636 c.136delG frameshift_variant 0.17
fbiB 3641806 p.Arg91His missense_variant 0.15
fbiB 3641844 p.Ala104Thr missense_variant 0.18
fbiB 3642092 c.560delT frameshift_variant 0.18
alr 3840305 c.1114_1115delGG frameshift_variant 0.14
alr 3841617 c.-197G>A upstream_gene_variant 0.17
rpoA 3878271 c.237T>C synonymous_variant 0.14
rpoA 3878284 p.Glu75Ala missense_variant 0.16
rpoA 3878292 c.216T>C synonymous_variant 0.15
rpoA 3878298 c.210A>G synonymous_variant 0.14
rpoA 3878304 c.204G>C synonymous_variant 0.17
rpoA 3878313 c.195G>C synonymous_variant 0.15
rpoA 3878322 c.186A>G synonymous_variant 0.15
rpoA 3878331 c.177A>G synonymous_variant 0.15
rpoA 3878334 c.174T>C synonymous_variant 0.14
rpoA 3878337 c.171T>C synonymous_variant 0.14
rpoA 3878346 c.162T>C synonymous_variant 0.15
rpoA 3878364 c.144A>T synonymous_variant 0.17
rpoA 3878367 c.141C>G synonymous_variant 0.17
rpoA 3878376 c.132G>C synonymous_variant 0.18
rpoA 3878385 c.123C>G synonymous_variant 0.18
rpoA 3878388 c.120C>G synonymous_variant 0.17
rpoA 3878391 c.117T>C synonymous_variant 0.17
clpC1 4038403 c.2302T>C synonymous_variant 0.2
clpC1 4038407 c.2298G>C synonymous_variant 0.2
clpC1 4038419 c.2286T>C synonymous_variant 0.18
clpC1 4038433 c.2272C>T synonymous_variant 0.2
clpC1 4038434 c.2271G>A synonymous_variant 0.2
clpC1 4038444 p.Ala754Lys missense_variant 0.22
clpC1 4038446 c.2259T>C synonymous_variant 0.22
clpC1 4038456 p.Val750Glu missense_variant 0.22
clpC1 4038460 p.Leu749Met missense_variant 0.22
clpC1 4038486 p.Gly740Asn missense_variant 0.2
clpC1 4038489 p.Ala739Gly missense_variant 0.2
clpC1 4038494 c.2211G>C synonymous_variant 0.2
clpC1 4038497 p.Ser736Gln missense_variant 0.25
clpC1 4038509 c.2196C>T synonymous_variant 0.3
clpC1 4038530 c.2175G>A synonymous_variant 0.3
clpC1 4038625 p.Lys694Glu missense_variant 0.14
clpC1 4038640 p.Asp689Asn missense_variant 0.13
clpC1 4039169 p.Glu512Asp missense_variant 0.11
clpC1 4039172 c.1533A>G synonymous_variant 0.12
clpC1 4039178 c.1527G>C synonymous_variant 0.12
clpC1 4039183 c.1522T>C synonymous_variant 0.12
clpC1 4039587 p.Ser373Leu missense_variant 0.15
clpC1 4039751 c.954A>G synonymous_variant 0.16
clpC1 4039979 c.726C>G synonymous_variant 0.12
clpC1 4039988 c.717C>G synonymous_variant 0.14
clpC1 4039991 c.714G>C synonymous_variant 0.13
clpC1 4040021 c.684A>C synonymous_variant 0.15
clpC1 4040024 c.681A>G synonymous_variant 0.17
clpC1 4040033 c.672G>C synonymous_variant 0.17
clpC1 4040551 c.154T>C synonymous_variant 0.25
embC 4240860 p.Leu333Arg missense_variant 1.0
embA 4244074 p.Ala281Asp missense_variant 0.18
embA 4245137 c.1905T>C synonymous_variant 0.12
embA 4245146 c.1914G>A synonymous_variant 0.12
embA 4245149 c.1917C>G synonymous_variant 0.12
embA 4245153 p.Ile641Val missense_variant 0.12
embA 4245182 c.1950T>C synonymous_variant 0.12
embB 4247322 p.Pro270Leu missense_variant 0.15
embB 4247773 c.1260G>A synonymous_variant 0.14
embB 4247776 c.1263G>T synonymous_variant 0.15
embB 4247797 c.1284C>G synonymous_variant 0.17
embB 4247800 c.1287A>T synonymous_variant 0.17
embB 4247803 c.1290G>C synonymous_variant 0.18
embB 4247815 c.1302C>G synonymous_variant 0.17
embB 4247819 p.Val436Ile missense_variant 0.17
embB 4247830 c.1317A>G synonymous_variant 0.17
embB 4247836 c.1323A>G synonymous_variant 0.2
embB 4247839 c.1326G>C synonymous_variant 0.2
embB 4247899 p.Met462Ile missense_variant 0.2
embB 4247945 c.1432T>C synonymous_variant 0.18
embB 4247951 p.Ser480Ala missense_variant 0.17
embB 4247956 c.1443G>C synonymous_variant 0.17
embB 4247974 c.1461C>G synonymous_variant 0.13
embB 4248007 c.1494C>G synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0