TB-Profiler result

Run: ERR245809
Summary

Run ID: ERR245809

Sample name:

Date: 31-03-2023 18:22:40

Number of reads: 8386399

Percentage reads mapped: 76.35

Strain: lineage4.3.4.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
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 5347 c.108G>C synonymous_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.3
ccsA 620748 c.858T>G synonymous_variant 0.25
rpoB 759831 p.Thr9Pro missense_variant 0.21
rpoB 762249 p.Leu815Val missense_variant 0.21
rpoC 762836 c.-534C>G upstream_gene_variant 0.33
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.12
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.14
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.18
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.17
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.15
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.11
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.12
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.12
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.11
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.1
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.14
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.16
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.21
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.23
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.11
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.1
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.15
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.18
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.18
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.18
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.18
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.19
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.19
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.12
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.12
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.1
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.11
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.11
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.11
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.11
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.21
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.2
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.13
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.13
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.16
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.17
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.17
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.14
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.12
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.14
rrl 1475154 n.1497C>A non_coding_transcript_exon_variant 0.14
rrl 1475167 n.1510T>A non_coding_transcript_exon_variant 0.11
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.11
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.14
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.28
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.3
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.3
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.49
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.43
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.22
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.1
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.12
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.13
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.13
fabG1 1673449 p.Thr4Pro missense_variant 0.37
inhA 1674892 p.Asn231Asp missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.22
PPE35 2168428 c.2184dupG frameshift_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.21
eis 2715586 c.-254G>C upstream_gene_variant 0.64
ahpC 2725954 c.-239C>T upstream_gene_variant 0.28
folC 2746186 c.1413G>C synonymous_variant 0.27
pepQ 2859381 c.1038C>G synonymous_variant 0.16
Rv2752c 3064741 p.Gly484Ala missense_variant 0.3
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611992 c.1125T>G synonymous_variant 0.62
Rv3236c 3612009 p.Ala370Thr missense_variant 0.99
fbiB 3640614 c.-921C>T upstream_gene_variant 1.0
fbiB 3642734 c.1200G>C synonymous_variant 0.29
rpoA 3877766 p.Ala248Pro missense_variant 0.3
ddn 3987013 p.Gly57Ala missense_variant 0.23
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.17
clpC1 4039363 p.Ala448Pro missense_variant 0.32
clpC1 4039932 p.Gly258Val missense_variant 0.2
embC 4241429 p.Phe523Val missense_variant 0.42
embC 4241456 p.Ala532Pro missense_variant 0.42
embC 4242425 p.Arg855Gly missense_variant 0.14
embC 4242476 p.Pro872Ala missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.39
embC 4242827 p.Leu989Val missense_variant 0.21
embA 4245329 c.2097A>G synonymous_variant 1.0
embB 4249504 p.Gln997His missense_variant 0.27
aftB 4268812 p.Ser9Ala missense_variant 0.31
aftB 4269411 c.-575T>C upstream_gene_variant 0.99
ubiA 4269529 p.Ala102Gly missense_variant 0.17
ethA 4327672 c.-199G>A upstream_gene_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.99