TB-Profiler result

Run: SRR1175096
Summary

Run ID: SRR1175096

Sample name:

Date: 03-04-2023 03:37:49

Number of reads: 1400022

Percentage reads mapped: 59.14

Strain: lineage1.2.2.2

Drug-resistance: Sensitive

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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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 0.98
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
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
gyrB 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 5151 c.-89C>A upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760735 p.Val310Gly missense_variant 1.0
rpoB 762233 c.2427G>C synonymous_variant 0.12
rpoB 762911 p.Ile1035Met missense_variant 0.11
rpoC 762920 c.-450C>T upstream_gene_variant 0.11
rpoC 762923 c.-447C>G upstream_gene_variant 0.11
rpoB 762942 p.Ile1046Val missense_variant 0.1
rpoC 762965 c.-405T>C upstream_gene_variant 0.19
rpoC 762989 c.-381G>T upstream_gene_variant 0.12
rpoC 762998 c.-372G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765398 p.Leu677Met missense_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
embR 1417019 p.Cys110Tyr missense_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.23
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.23
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.23
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.23
rrs 1472243 n.398G>A non_coding_transcript_exon_variant 0.2
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.21
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.2
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.26
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.13
rrs 1472279 n.434T>C non_coding_transcript_exon_variant 0.1
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.24
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.28
rrs 1472716 n.871C>G non_coding_transcript_exon_variant 0.28
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.45
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.44
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.49
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.51
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.51
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.48
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.12
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.18
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.22
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.37
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.38
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.38
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.29
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.36
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.23
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.29
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.29
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.21
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.22
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.3
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.24
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.24
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.12
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.12
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.12
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.3
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.32
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.4
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.52
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.42
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.48
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.1
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.17
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.17
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.17
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.17
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.17
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.17
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.17
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.31
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.14
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.43
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.43
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.56
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.49
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.45
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.45
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.59
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.52
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.43
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.67
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.64
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.64
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.56
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.47
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.47
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.42
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.42
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.46
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.51
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.19
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476669 n.3012C>T non_coding_transcript_exon_variant 0.98
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 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.37
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726193 c.1A>C initiator_codon_variant 1.0
ahpC 2726427 p.Asp79Asn missense_variant 1.0
pepQ 2860150 p.Ala90Val missense_variant 1.0
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
thyX 3067244 c.702C>T synonymous_variant 0.87
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244878 p.Ala549Val missense_variant 0.12
embA 4244910 p.Leu560Met missense_variant 0.11
embA 4245297 p.Pro689Ser missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268171 c.666G>A synonymous_variant 1.0
aftB 4268735 c.102C>G synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407973 p.Val77Ala missense_variant 0.29