TB-Profiler result

Run: ERR4815684
Summary

Run ID: ERR4815684

Sample name:

Date: 01-04-2023 14:00:25

Number of reads: 1764949

Percentage reads mapped: 90.64

Strain: lineage5.1.4

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
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 1.0
lineage5.1.4 West-Africa 1 AFRI_2;AFRI_3 RD711 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 0.73 streptomycin
gid 4408115 c.87delC frameshift_variant 1.0 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
gyrB 5416 c.177C>T synonymous_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763699 c.330G>T synonymous_variant 0.12
rpoC 763708 c.339G>C synonymous_variant 0.12
rpoC 763714 c.345G>C synonymous_variant 0.13
rpoC 763717 c.348T>C synonymous_variant 0.13
rpoC 763718 p.Leu117Val missense_variant 0.13
rpoC 763723 c.354G>C synonymous_variant 0.14
rpoC 763724 p.Asp119Asn missense_variant 0.14
rpoC 763729 c.360G>C synonymous_variant 0.14
rpoC 763732 c.363C>G synonymous_variant 0.14
rpoC 763735 c.366G>C synonymous_variant 0.14
rpoC 763751 p.Ile128Val missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775753 c.2727delC frameshift_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776109 p.Met791Thr missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.14
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.14
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.24
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.24
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.25
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.35
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.36
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.3
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.32
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.42
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.18
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.33
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.21
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.41
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.55
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.55
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.59
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.61
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.73
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.74
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.7
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.17
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.78
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.8
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.8
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.54
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.42
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.4
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.31
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 0.22
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.28
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.27
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.29
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.22
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.31
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.46
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.61
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.66
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.76
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.76
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.74
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.71
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.69
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.46
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.3
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.3
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.21
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.1
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.19
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.19
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.19
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.31
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.24
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.22
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.19
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.21
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.22
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.12
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.12
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.12
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.18
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.17
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.15
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.15
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473122 n.1278A>T non_coding_transcript_exon_variant 0.17
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.19
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.26
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.12
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.14
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.33
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.14
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.21
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.21
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.2
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.19
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.19
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.21
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.28
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.27
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.24
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.2
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.14
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.14
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.2
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.2
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.22
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.17
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.17
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.18
rrl 1474634 n.977T>C non_coding_transcript_exon_variant 0.13
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.15
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 0.14
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.14
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.14
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 0.13
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.11
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.12
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.23
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.23
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.14
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
ndh 2103112 c.-70G>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
Rv3083 3449507 p.Arg335Gln missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840932 c.489C>T synonymous_variant 1.0
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0
panD 4044182 p.Asp34Tyr missense_variant 0.11
embC 4239843 c.-20A>C upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244635 p.Val468Ala missense_variant 1.0
embA 4245147 p.Pro639Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4326928 c.-621G>A upstream_gene_variant 1.0
ethA 4327103 p.Gly124Asp missense_variant 1.0
whiB6 4338546 c.-25G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0