TB-Profiler result

Run: ERR4818355
Summary

Run ID: ERR4818355

Sample name:

Date: 01-04-2023 15:30:46

Number of reads: 805954

Percentage reads mapped: 90.36

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 0.66 streptomycin
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 8904 p.Arg535Cys missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490772 c.-11A>G upstream_gene_variant 0.12
fgd1 491173 p.Arg131Trp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576257 p.Ser304Gly missense_variant 0.13
mshA 576641 p.Asn432Tyr missense_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761542 p.Gln579Leu missense_variant 0.12
rpoB 762143 c.2337T>C synonymous_variant 0.17
rpoB 762149 c.2343G>C synonymous_variant 0.17
rpoB 762156 p.Val784Ile missense_variant 0.2
rpoB 762177 p.Arg791Thr missense_variant 0.2
rpoB 762181 p.Asp792Ala missense_variant 0.22
rpoB 762185 c.2379G>C synonymous_variant 0.22
rpoB 762194 c.2388G>C synonymous_variant 0.17
rpoB 762200 c.2394C>T synonymous_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762929 c.-441G>T upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763700 p.Pro111Thr missense_variant 0.1
rpoC 765590 p.Arg741Cys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776973 p.Met503Thr missense_variant 0.17
mmpL5 777032 c.1449C>G synonymous_variant 0.17
mmpL5 777035 c.1446G>A synonymous_variant 0.18
mmpL5 777191 c.1290C>A synonymous_variant 0.18
mmpL5 777196 p.Glu429Gln missense_variant 0.2
mmpL5 777735 p.Phe249Ser missense_variant 0.25
mmpL5 777820 c.661C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781760 c.201T>C synonymous_variant 0.13
rpsL 781766 c.207C>T synonymous_variant 0.13
rpsL 781772 c.213C>T synonymous_variant 0.19
rpsL 781796 p.Met79Ile missense_variant 0.22
rpsL 781802 c.243G>C synonymous_variant 0.2
rpsL 781811 c.252C>T synonymous_variant 0.2
rpsL 781814 c.255C>T synonymous_variant 0.2
rpsL 781817 c.258G>T synonymous_variant 0.19
fbiC 1304676 c.1746A>C synonymous_variant 1.0
Rv1258c 1406937 p.Ala135Val missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.67
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.8
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.82
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.82
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.82
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.82
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.91
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.87
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.81
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.54
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.69
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.25
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.69
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.69
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.69
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.69
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.72
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.83
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.75
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.67
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.67
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.67
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.5
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.38
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.5
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.75
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.5
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.62
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.62
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.25
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.67
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.55
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.44
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.25
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.38
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.44
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.44
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.44
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.44
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.71
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.4
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.33
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.29
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.33
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.18
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 1.0
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 1.0
rrl 1474634 n.977T>G non_coding_transcript_exon_variant 1.0
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 1.0
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.5
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.5
rrl 1475974 n.2317A>T non_coding_transcript_exon_variant 0.4
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.33
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.33
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.33
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.67
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.6
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.62
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.62
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.4
rpsA 1833727 c.186G>C synonymous_variant 0.18
rpsA 1833732 p.Pro64Leu missense_variant 0.2
rpsA 1833736 c.195C>T synonymous_variant 0.18
rpsA 1833742 c.201A>G synonymous_variant 0.18
rpsA 1834100 p.Arg187Cys missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918724 p.Arg262Leu missense_variant 0.12
ndh 2102167 p.Gln292His missense_variant 0.2
ndh 2103005 p.Arg13His missense_variant 0.22
katG 2153992 p.Leu707Arg missense_variant 1.0
katG 2154249 c.1863C>T synonymous_variant 0.2
katG 2154402 c.1710C>T synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167667 c.2945delT frameshift_variant 0.22
PPE35 2167729 p.Ala962Thr missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168651 p.Leu654Phe missense_variant 1.0
PPE35 2169182 c.1431G>A synonymous_variant 0.18
PPE35 2169683 c.930C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290125 c.-884C>T upstream_gene_variant 1.0
kasA 2518090 c.-25A>G upstream_gene_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860399 p.Arg7Gln missense_variant 1.0
Rv2752c 3066118 p.Asn25Ser missense_variant 0.12
ald 3086756 c.-64A>G upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087169 p.Tyr117Cys missense_variant 0.12
fbiD 3339218 p.Thr34Ile missense_variant 0.12
fbiD 3339366 c.249G>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474142 c.141dupG frameshift_variant 0.11
fprA 3475228 p.Asp408Asn missense_variant 0.13
Rv3236c 3612372 p.Leu249Phe missense_variant 0.15
fbiB 3642809 c.1275G>A synonymous_variant 0.13
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4040569 p.Ala46Thr missense_variant 0.11
clpC1 4040815 c.-111C>G upstream_gene_variant 0.11
embC 4240189 c.327G>C synonymous_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242184 c.2322C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243216 c.-17G>T upstream_gene_variant 0.11
embA 4243834 p.Ala201Val missense_variant 0.13
embB 4248067 p.Trp518Cys missense_variant 0.11
ubiA 4269124 p.Ala237Asp missense_variant 0.17
ethA 4327529 c.-56T>C upstream_gene_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407704 p.Ala167Thr missense_variant 0.18
gid 4408252 c.-50A>G upstream_gene_variant 0.12