TB-Profiler result

Run: ERR4831722
Summary

Run ID: ERR4831722

Sample name:

Date: 01-04-2023 21:04:56

Number of reads: 726965

Percentage reads mapped: 79.05

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491316 c.534C>G synonymous_variant 0.14
fgd1 491376 p.Lys198Asn missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576610 c.1263G>T synonymous_variant 0.25
ccsA 619865 c.-26G>T upstream_gene_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762257 c.2451C>A synonymous_variant 0.2
rpoB 762448 p.Gly881Val missense_variant 0.12
rpoC 762476 c.-894C>A upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763697 p.Val110Leu missense_variant 0.1
rpoC 764498 p.Ser377Ala missense_variant 0.12
rpoC 764503 c.1134G>T synonymous_variant 0.12
rpoC 764509 c.1140G>A synonymous_variant 0.12
rpoC 764513 p.Phe382Ile missense_variant 0.11
rpoC 764521 c.1152T>C synonymous_variant 0.12
rpoC 764666 p.Gly433Cys missense_variant 0.13
rpoC 767037 p.Ala1223Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777978 p.Ala168Glu missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779625 c.-720G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781640 p.Ser27Arg missense_variant 0.12
fbiC 1303157 p.His76Arg missense_variant 0.1
fbiC 1305033 c.2103T>A synonymous_variant 0.12
fbiC 1305061 p.Gly711Trp missense_variant 0.16
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407348 c.-8C>T upstream_gene_variant 1.0
embR 1416772 c.576C>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.32
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.31
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.3
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.28
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.34
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.32
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.32
rrs 1472679 n.834_835insAC non_coding_transcript_exon_variant 0.33
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.32
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.32
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.32
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.32
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.32
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.32
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.38
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.33
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.33
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.33
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.17
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.14
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.14
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.14
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.11
rrs 1472953 n.1108_1109insA non_coding_transcript_exon_variant 0.35
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.35
rrs 1472958 n.1114delT non_coding_transcript_exon_variant 0.35
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.29
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.29
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.29
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.29
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.32
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.32
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.34
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.34
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.25
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.14
rrl 1473787 n.130C>A non_coding_transcript_exon_variant 0.14
rrl 1473972 n.315G>A non_coding_transcript_exon_variant 0.18
rrl 1474670 n.1013C>A non_coding_transcript_exon_variant 0.97
rrl 1474922 n.1265G>T non_coding_transcript_exon_variant 0.12
rrl 1474990 n.1333C>A non_coding_transcript_exon_variant 0.11
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.11
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.12
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.12
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.15
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918080 c.141C>G synonymous_variant 0.15
tlyA 1918082 p.Asp48Val missense_variant 0.15
ndh 2101684 p.Gln453His missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154880 p.Ala411Asp missense_variant 0.12
katG 2155389 c.723C>A synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169938 c.675C>A synonymous_variant 0.13
PPE35 2170639 c.-27C>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289126 p.Ala39Gly missense_variant 0.12
folC 2746883 p.Pro239Gln missense_variant 0.15
folC 2747160 p.Pro147Ser missense_variant 0.12
folC 2747247 p.Ala118Ser missense_variant 0.12
pepQ 2860164 c.255C>A synonymous_variant 0.12
thyX 3067418 c.528C>A synonymous_variant 0.15
thyA 3074497 c.-26G>A upstream_gene_variant 0.14
thyA 3074533 c.-62G>A upstream_gene_variant 0.11
thyA 3074611 c.-140C>G upstream_gene_variant 0.12
thyA 3074650 c.-179G>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448968 c.465C>A synonymous_variant 0.12
Rv3083 3449040 p.Lys179Asn missense_variant 0.18
Rv3083 3449436 c.933G>T synonymous_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613071 p.Ala16Thr missense_variant 0.14
Rv3236c 3613081 c.36C>T synonymous_variant 0.14
fbiB 3641878 p.Arg115Gln missense_variant 0.15
fbiB 3642035 c.503_506delCCGG frameshift_variant 0.22
fbiB 3642105 p.Glu191* stop_gained 0.22
clpC1 4039437 p.Glu423Gly missense_variant 0.14
clpC1 4039570 p.Met379Leu missense_variant 1.0
embC 4240073 c.212dupA frameshift_variant 0.11
embC 4242139 c.2277G>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243706 c.474C>A synonymous_variant 0.13
embA 4244246 c.1014C>A synonymous_variant 0.15
embB 4246511 c.-3G>T upstream_gene_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269975 c.-142G>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0