TB-Profiler result

Run: SRR7131160
Summary

Run ID: SRR7131160

Sample name:

Date: 04-04-2023 18:47:24

Number of reads: 2160534

Percentage reads mapped: 99.98

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
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
gyrA 9596 c.2295G>T synonymous_variant 1.0
gyrA 9777 p.Asn826Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.12
mshA 576489 p.Val381Gly missense_variant 0.31
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762636 p.Lys944Glu missense_variant 1.0
rpoB 762872 p.Met1022Ile missense_variant 0.24
rpoB 762878 p.Ile1024Met missense_variant 0.29
rpoB 762879 p.Met1025Leu missense_variant 0.31
rpoC 762896 c.-474G>C upstream_gene_variant 0.36
rpoC 762917 c.-453C>G upstream_gene_variant 0.35
rpoC 762923 c.-447C>G upstream_gene_variant 0.35
rpoB 762925 p.Thr1040Ile missense_variant 0.35
rpoC 762929 c.-441G>C upstream_gene_variant 0.34
rpoB 762939 p.Met1045Leu missense_variant 0.29
rpoB 762942 p.Ile1046Val missense_variant 0.25
rpoC 762956 c.-414G>C upstream_gene_variant 0.21
rpoC 762965 c.-405T>C upstream_gene_variant 0.19
rpoC 762980 c.-390T>C upstream_gene_variant 0.18
rpoC 762989 c.-381G>C upstream_gene_variant 0.18
rpoC 762995 c.-375G>T upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 764582 p.Leu405Met missense_variant 0.12
rpoC 764587 c.1218C>G synonymous_variant 0.1
rpoC 764611 c.1242G>C synonymous_variant 0.26
rpoC 764632 c.1263T>C synonymous_variant 0.26
rpoC 764650 c.1281G>C synonymous_variant 0.23
rpoC 764665 c.1296C>T synonymous_variant 0.18
rpoC 764668 c.1299C>T synonymous_variant 0.18
rpoC 764671 c.1302G>C synonymous_variant 0.19
rpoC 764672 p.Gln435Glu missense_variant 0.18
rpoC 764677 c.1308C>G synonymous_variant 0.17
rpoC 764695 c.1326T>C synonymous_variant 0.19
rpoC 764701 c.1332C>G synonymous_variant 0.15
rpoC 764705 p.Leu446Lys missense_variant 0.14
rpoC 766981 c.3612T>G synonymous_variant 0.18
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 1472106 n.261G>A non_coding_transcript_exon_variant 0.36
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.44
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.45
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.45
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.46
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.44
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.45
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.48
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.47
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.48
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.71
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.77
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.71
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.67
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.67
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.64
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.65
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.63
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.63
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.34
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.16
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.15
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.33
rrs 1472349 n.504A>T non_coding_transcript_exon_variant 0.34
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.31
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.18
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.23
rrs 1472390 n.545T>C non_coding_transcript_exon_variant 0.21
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.28
rrs 1472398 n.553T>C non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.3
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.31
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.31
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.32
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.52
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.51
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.55
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.58
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.43
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.44
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.35
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.17
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.15
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 1473062 n.1217T>A non_coding_transcript_exon_variant 0.14
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.1
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.11
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.2
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.26
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.28
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.26
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.29
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.29
rrl 1474825 n.1168G>C non_coding_transcript_exon_variant 0.15
rrl 1474828 n.1171G>C non_coding_transcript_exon_variant 0.15
rrl 1474832 n.1176delG non_coding_transcript_exon_variant 0.15
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.15
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.11
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.15
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.14
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.27
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.31
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.1
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.55
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.66
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.66
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.72
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.74
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.73
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.75
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.76
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.64
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.69
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.67
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.7
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.7
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.59
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.56
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.51
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.34
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 2170065 p.Ala183Gly missense_variant 0.17
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714784 c.549C>T synonymous_variant 1.0
eis 2714915 c.418C>T synonymous_variant 1.0
eis 2715432 c.-100C>T upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568431 c.249C>G synonymous_variant 0.4
rpoA 3877752 c.756C>T synonymous_variant 1.0
clpC1 4040033 c.672G>C synonymous_variant 0.12
clpC1 4040090 c.615T>C synonymous_variant 0.11
clpC1 4040235 p.Gly157Ala missense_variant 0.29
embC 4240409 p.Pro183Ala missense_variant 0.22
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246553 c.43delG frameshift_variant 0.17
whiB6 4338200 p.Asp108His missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0