TB-Profiler result

Run: SRR11972331
Summary

Run ID: SRR11972331

Sample name:

Date: 03-04-2023 05:37:21

Number of reads: 940680

Percentage reads mapped: 94.81

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
katG 2155168 p.Ser315Thr missense_variant 0.38 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 490785 c.3G>T synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576390 p.Val348Ala missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760264 p.Met153Thr missense_variant 0.1
rpoB 761926 p.Met707Thr missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 0.5
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 778954 c.-474T>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
fbiC 1303285 p.Ser119Pro missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.16
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.16
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.16
rrs 1472606 n.761C>T non_coding_transcript_exon_variant 0.18
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrl 1474228 n.571T>A non_coding_transcript_exon_variant 0.12
rrl 1474779 n.1122G>C non_coding_transcript_exon_variant 0.13
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.18
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.16
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.16
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.3
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.21
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.25
rrl 1475175 n.1518G>A non_coding_transcript_exon_variant 0.14
rrl 1475182 n.1525T>G non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.13
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.13
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.13
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.32
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.37
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.29
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.25
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.35
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.27
rrl 1476427 n.2770G>T non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.21
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.27
fabG1 1673357 c.-83G>A upstream_gene_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.17
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834333 c.792C>T synonymous_variant 0.18
tlyA 1917796 c.-144C>T upstream_gene_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154396 c.1716G>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155457 p.Pro219Thr missense_variant 0.14
PPE35 2167745 p.Thr956Arg missense_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170189 p.Glu142Gln missense_variant 0.12
PPE35 2170196 c.417A>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.27
folC 2747437 p.Met54Ile missense_variant 0.71
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087446 c.627C>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.26
clpC1 4040144 c.561G>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
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
gid 4407934 p.Leu90Arg missense_variant 0.45