TB-Profiler result

Run: SRR1183958
Summary

Run ID: SRR1183958

Sample name:

Date: 03-04-2023 05:08:26

Number of reads: 624622

Percentage reads mapped: 13.3

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 0.85 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576068 p.Gly241Ser missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766667 p.Ser1100Pro missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.25
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.32
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.41
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.39
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.39
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.39
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.41
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.34
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.34
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.38
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.38
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.34
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.34
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.52
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.52
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.88
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.89
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.89
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.88
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.88
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.88
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.89
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.89
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.87
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.88
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.38
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.17
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.39
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.76
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.77
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.89
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.89
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.9
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.92
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.93
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.9
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.33
rrs 1473131 n.1286G>T non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.68
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.68
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.68
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.75
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.75
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.75
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.75
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.76
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.78
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.84
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.83
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.88
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.5
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.5
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.46
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.46
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.44
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.44
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.41
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.22
rrl 1474377 n.720G>T non_coding_transcript_exon_variant 0.17
rrl 1474842 n.1185G>T non_coding_transcript_exon_variant 0.12
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.12
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.12
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.11
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.13
rrl 1474903 n.1246T>A non_coding_transcript_exon_variant 0.13
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.13
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.12
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.13
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.3
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.3
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.26
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.26
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.27
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.27
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.1
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.1
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.25
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.76
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.88
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.89
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.91
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.91
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.93
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.92
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.96
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.96
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.95
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.95
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.95
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.92
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.7
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.39
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834347 p.Arg269Leu missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169221 c.1392T>C synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.33
PPE35 2170623 c.-11G>A upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290191 c.-950C>A upstream_gene_variant 0.12
eis 2714955 c.378C>T synonymous_variant 1.0
eis 2715123 c.210G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449279 p.Arg259Leu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612432 p.Val229Leu missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878202 c.306G>A synonymous_variant 0.15
ddn 3986718 c.-126A>G upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243661 c.429C>T synonymous_variant 0.25
embA 4245801 p.Tyr857His missense_variant 0.17
aftB 4267400 c.1437G>T synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268252 c.585G>T synonymous_variant 0.17
ethA 4327432 p.Ile14Met missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338711 c.-190C>A upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0