TB-Profiler result

Run: SRR1173727
Summary

Run ID: SRR1173727

Sample name:

Date: 03-04-2023 03:30:39

Number of reads: 855988

Percentage reads mapped: 72.56

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 0.99
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.His445Ser missense_variant 1.0 rifampicin
katG 2154007 c.2101_2104dupAACT frameshift_variant&stop_gained 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 576136 c.789T>C synonymous_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762911 p.Ile1035Met missense_variant 0.12
rpoC 762920 c.-450C>T upstream_gene_variant 0.11
rpoC 762923 c.-447C>G upstream_gene_variant 0.1
rpoB 762939 p.Met1045Leu missense_variant 0.11
rpoB 762942 p.Ile1046Val missense_variant 0.11
rpoC 762965 c.-405T>C upstream_gene_variant 0.13
rpoC 762989 c.-381G>C upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764665 c.1296C>G synonymous_variant 0.12
rpoC 764668 c.1299C>T synonymous_variant 0.12
rpoC 764695 c.1326T>C synonymous_variant 0.12
rpoC 764713 c.1344G>C synonymous_variant 0.13
rpoC 764719 c.1350G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305134 p.Gly735Val missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.16
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.19
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.17
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.18
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.17
rrs 1472243 n.398G>A non_coding_transcript_exon_variant 0.17
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.15
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.15
rrs 1472332 n.487_488insT non_coding_transcript_exon_variant 1.0
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>G non_coding_transcript_exon_variant 0.14
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.38
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.39
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.37
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.39
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.38
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.37
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.13
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.12
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18
rrs 1473201 n.1356A>T non_coding_transcript_exon_variant 0.18
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.18
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.3
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.42
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.41
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.41
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.4
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.37
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.35
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.35
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.35
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.43
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.37
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.25
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.26
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.23
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.23
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.23
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.19
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.15
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726115 c.-77delT upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613012 c.105G>T synonymous_variant 0.14
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244491 p.Thr420Met missense_variant 0.13
embB 4245629 c.-885C>T upstream_gene_variant 0.12
embB 4247990 p.Val493Leu missense_variant 0.83
ubiA 4268972 p.Ala288Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407847 p.Ala119Asp missense_variant 1.0