TB-Profiler result

Run: SRR12882020
Summary

Run ID: SRR12882020

Sample name:

Date: 03-04-2023 07:00:47

Number of reads: 2631026

Percentage reads mapped: 91.88

Strain: lineage3.1.1

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 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.71 streptomycin
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 0.99
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
rpoB 759834 p.Ala10Ser missense_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 0.85
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 776224 p.Gly753* stop_gained 0.24
mmpL5 778834 c.-354G>T upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304943 c.2013C>A synonymous_variant 0.25
embR 1417130 p.His73Arg missense_variant 0.11
embR 1417156 c.192A>G synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.1
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.13
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.29
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.34
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.34
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.46
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.47
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.54
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.51
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.36
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.32
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.28
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.39
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.21
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.22
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.18
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.27
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.26
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.26
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.25
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.26
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.34
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.37
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.49
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.49
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.45
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.53
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.65
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.65
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.68
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.49
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.45
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.38
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.16
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.19
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.28
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.38
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.35
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.26
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.3
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.27
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.23
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.5
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.5
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.73
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.77
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.39
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.3
rrl 1476156 n.2499C>A non_coding_transcript_exon_variant 0.27
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.23
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.38
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.29
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.29
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.27
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.27
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.25
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.24
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.24
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.24
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.75
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.83
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.85
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.8
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.79
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.79
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.77
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.78
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.79
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.76
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.72
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.66
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.51
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.31
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.18
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.17
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.17
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.17
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.17
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.21
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.29
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.33
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102308 c.735G>T synonymous_variant 0.24
ndh 2102977 c.66T>C synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154989 p.Pro375Thr missense_variant 0.27
katG 2155534 p.Pro193Arg missense_variant 0.17
katG 2156172 c.-61G>T upstream_gene_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170439 p.Gln58His missense_variant 0.26
PPE35 2170461 p.Gly51Glu 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 1.0
pncA 2289665 c.-424G>C upstream_gene_variant 0.12
pncA 2289894 c.-653G>T upstream_gene_variant 0.21
eis 2714323 p.Arg337His missense_variant 0.23
eis 2715208 p.Thr42Ile missense_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860181 c.238delG frameshift_variant 0.15
thyX 3067726 p.Glu74* stop_gained 0.29
thyX 3067778 c.168C>A synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474040 p.Gly12Trp missense_variant 0.22
whiB7 3568731 c.-52C>T upstream_gene_variant 0.25
whiB7 3568753 c.-74G>T upstream_gene_variant 0.25
Rv3236c 3612778 p.Leu113Phe missense_variant 0.25
Rv3236c 3612793 c.324C>A synonymous_variant 0.25
fbiA 3640520 c.-23G>T upstream_gene_variant 0.29
rpoA 3878583 c.-76C>A upstream_gene_variant 0.5
rpoA 3878592 c.-85C>A upstream_gene_variant 1.0
clpC1 4038885 p.Gly607Val missense_variant 0.33
clpC1 4039090 p.Leu539Met missense_variant 0.22
clpC1 4039949 c.756G>C synonymous_variant 0.1
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242333 p.Gly824Val missense_variant 0.29
embC 4242342 p.Thr827Met missense_variant 0.2
embA 4242352 c.-881G>T upstream_gene_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244716 p.Trp495Leu missense_variant 0.27
embA 4245286 p.Leu685Ser missense_variant 1.0
embB 4247491 c.978G>T synonymous_variant 0.29
aftB 4266997 p.Gly614Trp missense_variant 0.25
aftB 4268344 p.Arg165Ser missense_variant 0.22
aftB 4268622 p.Trp72Leu missense_variant 0.25
ethR 4327934 p.Ala129Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.96