TB-Profiler result

Run: SRR1173014
Summary

Run ID: SRR1173014

Sample name:

Date: 03-04-2023 03:14:57

Number of reads: 1518647

Percentage reads mapped: 58.17

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 0.97
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 0.98 rifampicin
katG 2154007 c.2101_2104dupAACT frameshift_variant&stop_gained 0.96 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 0.12 pyrazinamide
embB 4249583 p.Asp1024Asn missense_variant 0.29 ethambutol
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
rpoB 759746 c.-61C>T upstream_gene_variant 0.95
rpoB 761344 p.Val513Ala missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762899 c.-471G>C upstream_gene_variant 0.16
rpoB 762911 p.Ile1035Met missense_variant 0.24
rpoC 762920 c.-450C>T upstream_gene_variant 0.23
rpoC 762923 c.-447C>G upstream_gene_variant 0.24
rpoC 762929 c.-441G>T upstream_gene_variant 0.15
rpoB 762939 p.Met1045Leu missense_variant 0.21
rpoB 762942 p.Ile1046Val missense_variant 0.2
rpoC 762965 c.-405T>C upstream_gene_variant 0.2
rpoC 762980 c.-390T>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764623 c.1254C>G synonymous_variant 0.12
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764650 c.1281G>T synonymous_variant 0.25
rpoC 764665 c.1296C>G synonymous_variant 0.22
rpoC 764668 c.1299C>T synonymous_variant 0.21
rpoC 764695 c.1326T>C synonymous_variant 0.19
rpoC 764713 c.1344G>C synonymous_variant 0.15
rpoC 764719 c.1350G>A synonymous_variant 0.16
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.23
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.26
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.28
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.29
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.28
rrs 1472243 n.398G>A non_coding_transcript_exon_variant 0.27
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.24
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.25
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.27
rrs 1472332 n.487_488insT non_coding_transcript_exon_variant 1.0
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.24
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.29
rrs 1472716 n.871C>G non_coding_transcript_exon_variant 0.3
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.49
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.51
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.51
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.51
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.16
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.15
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.22
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.46
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.46
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.45
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.46
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.47
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.44
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.42
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.42
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.41
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.39
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.39
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.4
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.39
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.39
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.14
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.14
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.15
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.19
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.26
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.32
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.29
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.31
rrs 1473201 n.1356A>T non_coding_transcript_exon_variant 0.3
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.33
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.41
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.48
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.48
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.56
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.48
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.49
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.51
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.57
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.53
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.49
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.67
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.65
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.6
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.57
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.49
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.49
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.5
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.5
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.47
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.49
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
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 2169320 p.Leu431Phe missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.93
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726115 c.-77delT upstream_gene_variant 1.0
thyX 3067310 c.636C>G synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247990 p.Val493Leu missense_variant 0.57
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407847 p.Ala119Asp missense_variant 0.96