TB-Profiler result

Run: SRR6045997
Summary

Run ID: SRR6045997

Sample name:

Date: 04-04-2023 12:09:18

Number of reads: 2542670

Percentage reads mapped: 94.37

Strain: lineage3.1.3

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 1.0
lineage3.1.3 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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.14 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
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
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
mmpS5 778477 c.429A>T stop_lost&splice_region_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471728 n.-117delT upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.12
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.14
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.14
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.24
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.26
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.29
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.29
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.23
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.14
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.26
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.21
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.21
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.13
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.25
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.13
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.11
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.16
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.15
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.13
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.12
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.14
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.12
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.11
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.11
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 0.12
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.15
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.11
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.11
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.11
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.12
rrl 1474120 n.463A>T non_coding_transcript_exon_variant 0.18
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.14
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.16
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.16
rrl 1474353 n.696A>T non_coding_transcript_exon_variant 0.16
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.16
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.16
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.13
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.14
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.15
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.14
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.2
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.27
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.19
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.33
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.4
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.33
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.33
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.33
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.33
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.36
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.36
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.11
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.11
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.13
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.13
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.21
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.21
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.21
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.21
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.21
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.18
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.18
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.21
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.21
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.22
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.24
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.26
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.39
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.44
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.42
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.43
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.45
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.45
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.35
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.3
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rpsA 1834159 c.618G>A synonymous_variant 1.0
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 2222732 c.432delT frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612918 p.Val67Leu missense_variant 1.0
ddn 3987127 c.288delC frameshift_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244557 p.Arg442Lys missense_variant 0.98
embB 4249195 c.2682C>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408175 p.Ala10Pro missense_variant 1.0