TB-Profiler result

Run: SRR1173832
Summary

Run ID: SRR1173832

Sample name:

Date: 03-04-2023 03:32:31

Number of reads: 738172

Percentage reads mapped: 39.63

Strain: lineage4.6.1;lineage3.1

Drug-resistance: MDR-TB

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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 0.62
lineage4.6 Euro-American T;LAM None 0.25
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.6
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.21
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 0.33 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.38 isoniazid
katG 2155740 c.371delG frameshift_variant 0.33 isoniazid, isoniazid
embB 4247431 p.Met306Ile missense_variant 0.29 ethambutol
gid 4407851 c.351delG frameshift_variant 0.29 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 0.23
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7709 c.408G>A synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9439 p.Ser713* stop_gained 0.15
fgd1 491376 p.Lys198Asn missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 0.68
rpoB 759746 c.-61C>T upstream_gene_variant 0.79
rpoB 759772 c.-35C>A upstream_gene_variant 0.13
rpoB 761206 p.Arg467His missense_variant 0.12
rpoB 761679 p.Glu625Lys missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 0.75
rpoC 762917 c.-453C>G upstream_gene_variant 0.18
rpoC 762920 c.-450C>T upstream_gene_variant 0.18
rpoC 762923 c.-447C>G upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.56
rpoC 766003 c.2634G>T synonymous_variant 0.18
rpoC 766488 p.Pro1040Arg missense_variant 0.2
rpoC 766747 c.3378C>G synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.57
mmpL5 777333 p.Gly383Val missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304153 p.Pro408Leu missense_variant 0.18
Rv1258c 1406804 c.537G>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.11
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.23
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.38
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.22
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.26
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.18
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.25
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.31
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.49
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.32
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.17
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.43
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.23
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.39
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.17
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.16
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.17
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.15
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.12
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.15
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.13
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.14
rrs 1472427 n.582T>A non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.14
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.15
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.3
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.59
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.41
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.71
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.62
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.18
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.22
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.23
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.25
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.19
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.2
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.12
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.18
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17
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 0.2
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.2
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.22
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.2
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.22
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.2
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.2
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.21
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.2
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.2
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.2
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.2
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.17
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.17
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.45
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.62
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.56
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.72
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.47
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.18
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.7
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.11
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.8
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.53
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.7
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.77
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.68
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.7
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.58
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.71
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.72
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.62
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.74
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.16
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.51
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.25
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.15
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.13
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.13
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.13
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.13
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.14
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.13
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.14
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.14
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.14
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.13
fabG1 1673716 p.Ala93Leu missense_variant 0.13
rpsA 1833729 p.Ile63Asn missense_variant 0.12
rpsA 1833751 c.210C>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101777 c.1266C>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 0.45
katG 2155823 p.His97Asn missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 0.76
PPE35 2168293 p.Leu774Val missense_variant 0.12
PPE35 2169129 p.Asn495Ser missense_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.21
PPE35 2170461 p.Gly51Glu missense_variant 0.86
Rv1979c 2222795 c.369delC frameshift_variant 0.13
Rv1979c 2223155 p.Pro4Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289004 p.Asp80Tyr missense_variant 0.18
pncA 2289047 c.195C>T synonymous_variant 0.71
pncA 2289365 c.-125delC upstream_gene_variant 0.73
ahpC 2726105 c.-88G>A upstream_gene_variant 0.82
folC 2747130 p.Ala157Ser missense_variant 0.12
folC 2747575 c.24G>A synonymous_variant 0.17
ribD 2986765 c.-74G>T upstream_gene_variant 0.12
ribD 2987414 c.576C>A synonymous_variant 0.15
Rv2752c 3064809 c.1383C>A synonymous_variant 0.17
thyX 3067560 p.Arg129Leu missense_variant 0.15
thyA 3073869 p.Trp201Cys missense_variant 0.14
thyA 3073884 c.588C>A synonymous_variant 0.14
thyA 3074057 p.Glu139* stop_gained 0.18
thyA 3074342 p.Leu44Met missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 0.74
ald 3087283 p.Gly155Val missense_variant 0.33
fbiD 3339399 c.282C>A synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474177 c.171C>T synonymous_variant 0.27
fprA 3474786 c.780C>A synonymous_variant 0.15
whiB7 3568782 c.-103G>T upstream_gene_variant 0.12
fbiB 3641277 c.-258G>A upstream_gene_variant 0.14
fbiB 3641295 c.-240G>A upstream_gene_variant 0.12
rpoA 3878112 c.396C>A synonymous_variant 0.13
clpC1 4039381 p.Gln442Lys missense_variant 0.19
clpC1 4040835 c.-131G>T upstream_gene_variant 0.12
clpC1 4040867 c.-163A>T upstream_gene_variant 0.11
embC 4239686 c.-177C>A upstream_gene_variant 0.17
embC 4240172 p.Val104Met missense_variant 0.7
embC 4240932 p.Trp357Leu missense_variant 0.12
embC 4241138 p.Ala426Thr missense_variant 0.18
embC 4241562 p.Arg567His missense_variant 0.56
embC 4242075 p.Arg738Gln missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245355 p.Ala708Asp missense_variant 0.14
embB 4245962 c.-552G>A upstream_gene_variant 0.21
embB 4246921 c.408G>T synonymous_variant 0.29
embB 4248206 p.Ser565Gly missense_variant 0.25
embB 4248496 c.1983G>A synonymous_variant 0.14
embB 4249148 p.Ala879Ser missense_variant 0.17
aftB 4267019 c.1817delC frameshift_variant 0.12
aftB 4268519 c.318C>T synonymous_variant 0.33
aftB 4268921 c.-85C>T upstream_gene_variant 0.15
ubiA 4269472 p.Thr121Ile missense_variant 0.18
ethR 4326817 c.-732G>A upstream_gene_variant 0.14
ethR 4327595 p.Arg16Leu missense_variant 0.15
ethA 4328329 c.-856C>G upstream_gene_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.73
gid 4407742 p.Arg154Gln missense_variant 0.39
gid 4408069 p.Trp45Leu missense_variant 0.14