TB-Profiler result

Run: ERR2843513
Summary

Run ID: ERR2843513

Sample name:

Date: 31-03-2023 23:51:48

Number of reads: 1147974

Percentage reads mapped: 62.72

Strain: lineage2.2.1;lineage1.1.1

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
lineage1 Indo-Oceanic EAI RD239 0.14
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.8
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.82
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.12
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 781822 p.Lys88Arg missense_variant 0.6 streptomycin
eis 2715339 c.-8delC upstream_gene_variant 0.12 kanamycin
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 5813 p.Arg192Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9485 c.2189delG frameshift_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.7
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 620561 p.Thr224Ile missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761475 p.Arg557Cys missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763678 p.His103Gln missense_variant 0.14
rpoC 763884 p.Ala172Val missense_variant 0.13
rpoC 765466 c.2097C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775811 c.2670C>T synonymous_variant 0.17
mmpL5 775978 p.Val835Met missense_variant 0.15
mmpL5 775979 p.Leu834Phe missense_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.83
mmpL5 776453 p.Met676Ile missense_variant 0.15
mmpL5 778231 p.Glu84Lys missense_variant 0.14
mmpR5 778298 c.-692C>A upstream_gene_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801116 p.Ala103Glu missense_variant 0.25
rplC 801298 c.493delC frameshift_variant 0.12
fbiC 1303330 p.Arg134* stop_gained 0.15
fbiC 1303539 c.609G>T synonymous_variant 0.18
fbiC 1303580 p.Thr217Met missense_variant 0.22
Rv1258c 1406680 c.660delG frameshift_variant 0.5
Rv1258c 1406701 p.Glu214Lys missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 0.71
embR 1416755 p.Thr198Arg missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 0.18
embR 1417273 c.75C>A synonymous_variant 0.18
embR 1417312 c.36C>T synonymous_variant 0.18
atpE 1460891 c.-154G>A upstream_gene_variant 0.18
atpE 1460938 c.-107C>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471764 n.-82C>T upstream_gene_variant 0.14
rrs 1471772 n.-74G>T upstream_gene_variant 0.17
rrs 1471788 n.-58G>A upstream_gene_variant 0.14
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.33
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.33
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.33
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.5
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.4
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.75
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.75
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.67
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.67
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.67
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.67
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.67
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.8
rrs 1472566 n.721G>T non_coding_transcript_exon_variant 0.29
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.71
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.71
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.71
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.71
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.67
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.67
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.5
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.4
rrl 1474747 n.1090C>A non_coding_transcript_exon_variant 0.18
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.18
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.33
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.33
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.33
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.36
rrl 1474797 n.1140_1141insTATA non_coding_transcript_exon_variant 0.4
rrl 1474800 n.1144_1147delGTGC non_coding_transcript_exon_variant 0.4
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.43
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.46
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.46
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.46
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.46
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.53
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.12
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.53
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.47
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.45
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.4
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.4
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.38
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.29
rrl 1475091 n.1434G>A non_coding_transcript_exon_variant 0.5
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.29
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.29
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.29
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.29
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.29
rrl 1475880 n.2223C>T non_coding_transcript_exon_variant 0.67
rrl 1475882 n.2225C>T non_coding_transcript_exon_variant 0.67
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>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 0.88
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.88
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.88
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.88
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.88
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.88
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.88
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.88
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.88
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.88
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.88
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.89
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.82
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.82
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.8
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.8
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.8
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.83
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.8
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.8
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.8
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.82
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.8
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.88
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.83
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.83
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.83
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.83
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.83
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.83
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.71
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.71
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.71
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.71
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.71
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.67
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.67
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.67
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.67
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.5
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.4
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.4
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.4
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.5
rpsA 1833680 p.Asp47Asn missense_variant 0.18
rpsA 1833963 p.Asp141Gly missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.5
rpsA 1834271 p.His244Tyr missense_variant 0.12
rpsA 1834319 p.Val260Ile missense_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102081 p.Gly321Val missense_variant 0.14
ndh 2102635 c.408C>T synonymous_variant 0.2
ndh 2102712 p.Pro111Thr missense_variant 0.33
katG 2153995 p.Ala706Glu missense_variant 0.2
katG 2154259 p.Thr618Met missense_variant 0.14
katG 2154672 c.1440G>A synonymous_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155887 c.225C>T synonymous_variant 0.14
katG 2156012 p.Gly34Arg missense_variant 0.17
katG 2156198 c.-87G>T upstream_gene_variant 0.5
katG 2156452 c.-341G>T upstream_gene_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167982 c.2631C>A synonymous_variant 0.2
PPE35 2168009 p.Ser868Arg missense_variant 0.15
PPE35 2169017 p.Leu532Phe missense_variant 0.25
PPE35 2169382 p.Trp411Arg missense_variant 0.2
PPE35 2169544 p.Gly357Cys missense_variant 0.29
PPE35 2170701 c.-89C>T upstream_gene_variant 0.22
Rv1979c 2221889 p.Val426Ile missense_variant 0.75
Rv1979c 2222308 p.Asp286Gly missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289086 c.156C>T synonymous_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 0.22
kasA 2519275 c.1161C>T synonymous_variant 0.14
eis 2714206 p.Arg376Leu missense_variant 0.12
eis 2715293 p.Pro14Ser missense_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 0.18
ahpC 2726157 c.-36C>T upstream_gene_variant 0.14
ribD 2986717 c.-122G>T upstream_gene_variant 0.12
Rv2752c 3065086 p.Arg369Met missense_variant 0.12
Rv2752c 3065236 p.Ser319* stop_gained 0.18
thyA 3073859 p.Asp205Asn missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.13
Rv3083 3448505 c.2T>C start_lost 0.18
Rv3083 3449561 p.Leu353Pro missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474063 c.57G>C synonymous_variant 0.15
fprA 3474361 p.Leu119Met missense_variant 0.2
fprA 3474597 c.591C>A synonymous_variant 0.29
fprA 3475159 p.Asn385Asp missense_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 0.92
alr 3840241 p.Pro394Thr missense_variant 0.15
clpC1 4038326 c.2379G>A synonymous_variant 0.17
clpC1 4038853 p.Pro618Ser missense_variant 0.14
clpC1 4039228 p.Gly493Cys missense_variant 0.12
clpC1 4040432 c.273C>T synonymous_variant 0.13
clpC1 4040457 c.247delC frameshift_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 0.46
embC 4240671 p.Thr270Ile missense_variant 0.4
embC 4241042 p.Asn394Asp missense_variant 0.14
embC 4241963 p.Ala701Ser missense_variant 0.15
embC 4241982 p.Pro707Leu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243326 p.Pro32Ser missense_variant 0.14
embA 4243460 c.228C>T synonymous_variant 0.63
embA 4243848 p.Val206Met missense_variant 0.21
embA 4244096 c.864C>T synonymous_variant 0.3
embA 4245124 p.Gly631Val missense_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 0.12
embA 4246085 p.Glu951Asp missense_variant 0.9
embB 4247313 p.Arg267Pro missense_variant 0.3
embB 4247646 p.Glu378Ala missense_variant 0.27
embB 4248433 p.Trp640Cys missense_variant 0.2
embB 4249557 p.Thr1015Ile missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.74
aftB 4268456 c.381G>A synonymous_variant 0.9
ubiA 4269109 p.Gly242Val missense_variant 0.12
ubiA 4269193 p.Thr214Ile missense_variant 0.17
aftB 4269474 c.-638G>T upstream_gene_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 0.25
ethA 4327083 p.Cys131Ser missense_variant 0.15
ethR 4327099 c.-450C>T upstream_gene_variant 0.13
ethR 4327745 p.Pro66Gln missense_variant 0.17
ethA 4328312 c.-839C>T upstream_gene_variant 0.14
whiB6 4338242 p.Gln94Glu missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.16
gid 4407927 p.Glu92Asp missense_variant 0.78