TB-Profiler result

Run: SRR11349180
Summary

Run ID: SRR11349180

Sample name:

Date: 02-04-2023 20:54:48

Number of reads: 4385913

Percentage reads mapped: 87.85

Strain: lineage2.2.1

Drug-resistance: MDR-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 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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761265 p.Asn487His missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 1472172 n.327T>C non_coding_transcript_exon_variant 0.1
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.15
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.11
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.19
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.19
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.21
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.13
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.13
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.14
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.36
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.13
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.12
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.36
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.13
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.19
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.1
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.14
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.14
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.14
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.14
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.17
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.17
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.17
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.18
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.17
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.17
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.17
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.1
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.1
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.11
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.14
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.14
rrl 1474658 n.1001A>G non_coding_transcript_exon_variant 0.12
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.12
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.12
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.12
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.12
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.11
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.14
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.18
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.23
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.17
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.43
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.31
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.48
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.17
rrl 1476404 n.2747G>A non_coding_transcript_exon_variant 0.16
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.35
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.15
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.19
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.16
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.16
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.16
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 1.0
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 2169029 p.Asp528Glu missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878619 c.-112A>C upstream_gene_variant 0.15
rpoA 3878629 c.-122A>C upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246469 c.-45C>A upstream_gene_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0