TB-Profiler result

Run: ERR4815551
Summary

Run ID: ERR4815551

Sample name:

Date: 01-04-2023 13:55:43

Number of reads: 744281

Percentage reads mapped: 44.26

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.76 streptomycin
pncA 2288844 p.Ile133Thr missense_variant 0.12 pyrazinamide
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 7391 c.91_98delTATGCGAT frameshift_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490986 c.204G>T synonymous_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576741 p.Ala465Glu missense_variant 0.17
ccsA 620194 p.Thr102Ala missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761435 c.1629T>C synonymous_variant 0.14
rpoB 761438 c.1632G>T synonymous_variant 0.14
rpoB 761441 p.Asp545Glu missense_variant 0.14
rpoB 761444 c.1638T>C synonymous_variant 0.17
rpoB 761447 c.1641C>G synonymous_variant 0.15
rpoB 761471 c.1665C>G synonymous_variant 0.13
rpoB 761483 c.1677G>C synonymous_variant 0.11
rpoC 762782 c.-588T>C upstream_gene_variant 0.18
rpoB 762799 p.Ala998Gly missense_variant 0.12
rpoC 762812 c.-558C>G upstream_gene_variant 0.11
rpoB 762813 p.Met1003Val missense_variant 0.11
rpoC 762902 c.-468C>T upstream_gene_variant 0.13
rpoC 762911 c.-459C>T upstream_gene_variant 0.13
rpoC 762917 c.-453C>T upstream_gene_variant 0.12
rpoC 762920 c.-450C>T upstream_gene_variant 0.12
rpoC 762929 c.-441G>T upstream_gene_variant 0.12
rpoC 762944 c.-426C>T upstream_gene_variant 0.16
rpoC 762956 c.-414G>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764939 p.Leu524Met missense_variant 0.11
rpoC 765236 p.Asp623Asn missense_variant 0.12
rpoC 766891 c.3527delT frameshift_variant 0.15
rpoC 766918 c.3549C>A synonymous_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 777704 c.777G>A synonymous_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781658 c.99A>G synonymous_variant 0.13
rpsL 781667 c.108C>T synonymous_variant 0.14
rpsL 781682 c.123T>C synonymous_variant 0.11
fbiC 1303893 c.963G>T synonymous_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416847 c.501A>T synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.24
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.23
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.23
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.29
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.68
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.63
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.38
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.4
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.5
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.68
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.68
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.35
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.54
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.35
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.9
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.87
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.86
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.88
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.88
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.35
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.64
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.58
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.42
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.37
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.31
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.42
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.38
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.36
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.38
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.38
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.38
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.59
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.71
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.71
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.76
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.78
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.78
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.12
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.76
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.76
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.62
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.29
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.29
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.34
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.42
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.53
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.62
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.58
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.7
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.57
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.55
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.66
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.5
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.41
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.42
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.45
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.49
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.46
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.44
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.44
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.46
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.46
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.46
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.49
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.35
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.14
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.14
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.17
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.19
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.18
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.5
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.21
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.53
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.24
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.11
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.5
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.16
rrs 1473291 n.1446G>A non_coding_transcript_exon_variant 0.23
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.3
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.21
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.19
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.19
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.12
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.12
rrl 1474074 n.417C>T non_coding_transcript_exon_variant 0.11
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.27
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.45
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.41
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.18
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.65
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.21
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.65
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.62
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.18
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.16
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.54
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.13
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.74
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.71
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.14
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.14
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.14
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.15
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.15
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.15
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.18
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
inhA 1674210 c.9A>C synonymous_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917965 p.Ala9Val missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917975 c.36C>G synonymous_variant 0.22
tlyA 1917981 c.42G>C synonymous_variant 0.2
tlyA 1917987 c.48G>C synonymous_variant 0.22
tlyA 1917996 c.57A>C synonymous_variant 0.2
tlyA 1918002 p.Gln21His missense_variant 0.17
ndh 2101843 p.His400Gln missense_variant 0.12
ndh 2102861 p.Gly61Ala missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170050 p.Ala188Glu missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289173 c.69T>C synonymous_variant 0.5
kasA 2518871 p.His253Asn missense_variant 0.18
folC 2746433 p.Gly389Val missense_variant 0.14
Rv2752c 3067030 c.-839C>T upstream_gene_variant 0.14
thyX 3067602 p.Arg115Gln missense_variant 0.18
thyX 3067750 p.Asp66Asn missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087317 c.498C>A synonymous_variant 0.15
Rv3083 3448426 c.-78T>C upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474882 p.Asn292Lys missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640803 c.-732C>T upstream_gene_variant 1.0
fbiB 3640920 c.-615A>G upstream_gene_variant 0.17
fbiB 3640989 c.-546T>C upstream_gene_variant 0.14
fbiB 3642865 p.Leu444Ser missense_variant 0.18
alr 3840256 p.Glu389Lys missense_variant 0.12
clpC1 4038670 p.Leu679Met missense_variant 0.11
clpC1 4039293 p.Gly471Val missense_variant 0.13
clpC1 4039596 p.His370Leu missense_variant 0.22
embC 4239983 p.Ala41Thr missense_variant 0.22
embC 4241195 p.Ser445Pro missense_variant 0.14
embC 4241306 p.Val482Ile missense_variant 0.14
embC 4242331 c.2474delG frameshift_variant 0.17
embA 4242352 c.-881G>C upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244513 c.1281C>A synonymous_variant 0.29
embA 4245536 c.2307delC frameshift_variant 0.13
embB 4245566 c.-948C>T upstream_gene_variant 0.15
embB 4245683 c.-831C>T upstream_gene_variant 0.14
embA 4245693 p.Ile821Val missense_variant 0.31
embB 4245714 c.-800C>T upstream_gene_variant 0.18
embB 4245725 c.-789A>G upstream_gene_variant 0.18
embB 4245726 c.-788T>C upstream_gene_variant 0.18
embB 4248461 p.Ser650Pro missense_variant 0.12
embB 4248633 p.Val707Ala missense_variant 0.15
aftB 4267265 c.1572C>T synonymous_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267704 p.Leu378Pro missense_variant 0.13
ethA 4328133 c.-660C>T upstream_gene_variant 0.17
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