TB-Profiler result

Run: SRR6896539
Summary

Run ID: SRR6896539

Sample name:

Date: 04-04-2023 18:09:15

Number of reads: 689648

Percentage reads mapped: 84.57

Strain: lineage3

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.47 streptomycin
inhA 1674319 p.Gly40Trp missense_variant 0.12 isoniazid
katG 2155793 p.Trp107Arg missense_variant 0.2 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 8056 p.Arg252Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620062 p.Ser58Arg missense_variant 0.2
ccsA 620209 c.323delG frameshift_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761297 p.Tyr497* stop_gained 0.12
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
mmpL5 779157 c.-677C>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303646 p.Ala239Glu missense_variant 0.17
embR 1417102 c.246C>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.19
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.17
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.17
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.23
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.34
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.31
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.37
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.34
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.38
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.35
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.34
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.32
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.34
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.31
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.23
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.23
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.23
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.18
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.17
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.16
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.19
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.18
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.17
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.13
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.12
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.14
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.16
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.16
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.26
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.29
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.38
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.38
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.43
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.43
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.28
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.28
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.25
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.28
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.31
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.3
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.34
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.53
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.54
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.47
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.38
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.15
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.16
rrs 1472826 n.981G>A non_coding_transcript_exon_variant 0.15
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.15
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.15
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.17
rrs 1472838 n.993A>T non_coding_transcript_exon_variant 0.15
rrs 1472845 n.1000G>C non_coding_transcript_exon_variant 0.17
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.17
rrs 1472873 n.1028C>A non_coding_transcript_exon_variant 0.18
rrs 1472875 n.1030T>A non_coding_transcript_exon_variant 0.2
rrs 1472877 n.1032T>A non_coding_transcript_exon_variant 0.18
rrs 1472880 n.1035_1036insA non_coding_transcript_exon_variant 0.17
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.28
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.11
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.1
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.18
rrl 1474053 n.396G>A non_coding_transcript_exon_variant 0.12
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.19
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.18
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.18
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.18
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.18
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.18
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.21
rrl 1474903 n.1246T>A non_coding_transcript_exon_variant 0.21
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.21
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.19
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.19
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.15
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.14
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.23
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.28
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.45
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.48
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.5
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.54
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.54
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.5
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.48
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.48
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.48
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.48
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.48
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.46
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.52
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.52
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.46
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.58
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.65
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.63
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.63
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.64
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.64
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.64
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.65
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.65
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.65
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.66
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.65
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.63
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.49
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.39
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.38
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.38
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.36
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.36
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.36
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.38
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.38
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.38
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.39
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.41
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.41
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.36
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.36
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.38
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.13
fabG1 1673515 p.Gly26Arg missense_variant 0.12
fabG1 1673518 p.Ile27Val missense_variant 0.12
rpsA 1834909 c.1368G>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101679 p.Ser455* stop_gained 0.18
ndh 2102583 p.Ala154Ser missense_variant 0.12
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 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.92
pncA 2289478 c.-237T>A upstream_gene_variant 0.17
kasA 2518647 p.Ile178Thr missense_variant 0.11
eis 2715139 p.Met65Thr missense_variant 0.12
eis 2715311 p.Pro8Thr missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859620 p.Gly267Cys missense_variant 0.12
pepQ 2860113 c.306C>A synonymous_variant 0.13
pepQ 2860184 c.229_234delCGCGCG conservative_inframe_deletion 0.12
pepQ 2860201 c.216_217delAG frameshift_variant 0.12
pepQ 2860207 c.211_212insGCGCGC conservative_inframe_insertion 0.13
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339324 c.207G>A synonymous_variant 0.12
Rv3083 3448897 p.Thr132Ala missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474655 p.Asp217His missense_variant 0.1
Rv3236c 3612843 c.273delG frameshift_variant 0.13
fbiB 3640629 c.-906T>C upstream_gene_variant 0.14
fbiB 3642412 p.Arg293Pro missense_variant 0.11
clpC1 4038843 p.Val621Ala missense_variant 0.11
clpC1 4039669 p.Gln346* stop_gained 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243285 p.Val18Ala missense_variant 0.11
embA 4243292 c.60G>T synonymous_variant 0.12
embA 4244480 c.1248G>A synonymous_variant 0.13
embA 4244638 p.Val469Ala missense_variant 0.21
embB 4245824 c.-690G>A upstream_gene_variant 0.17
embB 4247141 p.Phe210Leu missense_variant 0.11
aftB 4268683 p.Gly52Cys missense_variant 0.18
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0