TB-Profiler result

Run: ERR2179834
Summary

Run ID: ERR2179834

Sample name:

Date: 15-08-2022 11:56:12

Number of reads: 2808808

Percentage reads mapped: 86.02

Strain: lineage3

Drug-resistance: Other

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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
gyrA 7570 p.Ala90Val missense_variant 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779315 p.Arg109Leu missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304293 p.Thr455Ala missense_variant 1.0
embR 1416373 c.975C>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.12
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.13
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.13
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.13
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.13
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.13
rrl 1474797 n.1140_1141insTATA non_coding_transcript_exon_variant 0.14
rrl 1474800 n.1144_1147delGTGC non_coding_transcript_exon_variant 0.14
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.14
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.14
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.15
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.17
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.18
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.09
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.1
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.11
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.11
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.11
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.14
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.11
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.12
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.12
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.11
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.12
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.13
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.15
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.38
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.36
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.34
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.26
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.24
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.23
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.24
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.23
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.22
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.22
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.21
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.21
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.34
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.4
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
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 2289047 c.195C>T synonymous_variant 0.98
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747020 c.579C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246567 c.54G>T synonymous_variant 0.97
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408156 p.Leu16Pro missense_variant 0.65