TB-Profiler result

Run: SRR1173293
Summary

Run ID: SRR1173293

Sample name:

Date: 03-04-2023 03:21:01

Number of reads: 888127

Percentage reads mapped: 39.8

Strain: lineage4.6.1;lineage3.1.1

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 0.72
lineage4 Euro-American LAM;T;S;X;H None 0.35
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.88
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.72
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.29
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 761155 p.Ser450Leu missense_variant 0.29 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.14 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.54 ethambutol
gid 4407851 c.351delG frameshift_variant 0.86 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 7539 p.Thr80Ala missense_variant 0.35
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7709 c.408G>A synonymous_variant 0.36
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490599 c.-184C>A upstream_gene_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 0.74
mshA 575320 c.-28C>T upstream_gene_variant 0.12
mshA 575640 p.Pro98Gln missense_variant 0.15
ccsA 620799 p.Met303Ile missense_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 0.64
rpoB 761270 c.1464C>A synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 0.69
rpoC 764021 c.652C>A synonymous_variant 0.13
rpoC 764566 c.1197C>G synonymous_variant 0.27
rpoC 764575 c.1206T>G synonymous_variant 0.27
rpoC 764581 c.1212T>C synonymous_variant 0.3
rpoC 764582 p.Leu405Met missense_variant 0.3
rpoC 764587 c.1218C>G synonymous_variant 0.36
rpoC 764593 c.1224C>T synonymous_variant 0.36
rpoC 764605 c.1236G>C synonymous_variant 0.31
rpoC 764611 c.1242G>T synonymous_variant 0.31
rpoC 764632 c.1263T>C synonymous_variant 0.29
rpoC 764641 c.1272C>T synonymous_variant 0.26
rpoC 764650 c.1281G>T synonymous_variant 0.29
rpoC 764663 p.Val432Thr missense_variant 0.18
rpoC 764672 p.Gln435Glu missense_variant 0.12
rpoC 764677 c.1308C>G synonymous_variant 0.12
rpoC 764695 c.1326T>C synonymous_variant 0.12
rpoC 765191 c.1823delA frameshift_variant 0.13
rpoC 766488 p.Pro1040Arg missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.53
mmpL5 778516 c.-36C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406390 p.Leu317Phe missense_variant 0.12
embR 1416634 p.Asp238Glu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.12
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.12
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.12
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.12
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.12
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.23
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.32
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.26
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.22
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.37
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.26
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.15
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.16
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.23
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.35
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.21
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.13
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.28
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.12
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.29
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.18
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.18
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.14
rrs 1472427 n.582T>A non_coding_transcript_exon_variant 0.36
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.2
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.12
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.17
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.17
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.15
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.16
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.15
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.15
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.54
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.38
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.54
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.12
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.12
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.42
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.15
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.16
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.23
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.31
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.54
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.38
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.17
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.16
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.56
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.32
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.17
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.33
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.1
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.17
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.16
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.17
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.17
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.17
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.23
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.19
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.17
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.16
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.17
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.16
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.32
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.32
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.32
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.32
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.33
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.31
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.31
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.3
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.3
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.3
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.3
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.3
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.4
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.57
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.48
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.61
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.43
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.16
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.59
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.41
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.42
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.62
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.79
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.75
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.51
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.42
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.64
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.62
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.44
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.6
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.19
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.12
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.12
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
inhA 1674281 p.Arg27Leu missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102623 c.420C>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.82
PPE35 2167926 p.Leu896Ser missense_variant 0.84
PPE35 2169320 p.Leu431Phe missense_variant 0.21
PPE35 2170461 p.Gly51Glu missense_variant 0.56
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.56
pncA 2289365 c.-125delC upstream_gene_variant 0.64
kasA 2518593 p.Ala160Asp missense_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 0.71
folC 2747535 p.Asp22Tyr missense_variant 0.15
pepQ 2860142 p.Gly93Arg missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.7
fbiD 3339140 p.Gly8Asp missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474177 c.171C>T synonymous_variant 0.24
Rv3236c 3613149 c.-33G>A upstream_gene_variant 0.15
Rv3236c 3613153 c.-37G>T upstream_gene_variant 0.15
fbiA 3641494 p.Glu318Lys missense_variant 0.15
rpoA 3878703 c.-196G>A upstream_gene_variant 0.14
ddn 3987011 c.168C>T synonymous_variant 0.12
embC 4240172 p.Val104Met missense_variant 0.64
embC 4240728 p.Ala289Val missense_variant 0.12
embC 4241562 p.Arg567His missense_variant 0.44
embC 4242075 p.Arg738Gln missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4266975 p.Pro621His missense_variant 0.12
ubiA 4269670 p.Val55Gly missense_variant 0.33
ethA 4326038 p.Arg479Leu missense_variant 0.12
ethA 4328329 c.-856C>G upstream_gene_variant 0.56
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.79
gid 4407742 p.Arg154Gln missense_variant 0.41