TB-Profiler result

Run: SRR1173565
Summary

Run ID: SRR1173565

Sample name:

Date: 03-04-2023 03:27:46

Number of reads: 959258

Percentage reads mapped: 41.15

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
lineage4 Euro-American LAM;T;S;X;H None 0.36
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.8
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.32
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 0.4 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.19 ethambutol
gid 4407851 c.351delG frameshift_variant 0.33 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 0.36
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9621 c.2320C>T synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 0.81
ccsA 620052 c.162G>A synonymous_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 0.63
rpoC 762434 c.-936T>G upstream_gene_variant 0.82
rpoC 762887 c.-483G>C upstream_gene_variant 0.12
rpoC 762899 c.-471G>C upstream_gene_variant 0.11
rpoC 762917 c.-453C>G upstream_gene_variant 0.15
rpoC 762920 c.-450C>T upstream_gene_variant 0.14
rpoC 762923 c.-447C>G upstream_gene_variant 0.14
rpoB 762925 p.Thr1040Ile missense_variant 0.15
rpoB 762934 c.3129_3130insAGCC frameshift_variant 0.13
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.48
rpoC 764781 p.Ser471Thr missense_variant 0.1
rpoC 764806 p.Gln479His missense_variant 0.11
rpoC 764815 c.1446A>G synonymous_variant 0.1
rpoC 765179 p.Gly604Trp missense_variant 0.15
rpoC 766488 p.Pro1040Arg missense_variant 0.35
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304236 p.Gln436Lys missense_variant 0.15
fbiC 1304570 p.Val547Glu missense_variant 0.12
fbiC 1304670 c.1740G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.12
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.13
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.14
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.19
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.28
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.21
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.23
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.38
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.25
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.15
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.13
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.16
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.28
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.36
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.17
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.24
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.14
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.21
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.1
rrs 1472427 n.582T>A non_coding_transcript_exon_variant 0.5
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.15
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.22
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.18
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.22
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.12
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.2
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.24
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.14
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.14
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.14
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.15
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 0.15
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.16
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.19
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.1
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.2
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.22
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.25
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.18
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.65
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.1
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.31
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.2
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.68
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.55
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.23
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.15
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.25
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.19
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.28
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.34
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.27
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.33
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.28
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.27
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.2
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.17
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.22
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.19
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.16
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.14
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.19
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.18
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.21
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.13
rrl 1475106 n.1449G>T non_coding_transcript_exon_variant 0.12
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.28
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.24
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.24
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.24
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.24
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.24
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.24
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.23
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.24
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.24
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.25
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.25
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.16
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.14
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.14
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.18
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.16
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.15
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.11
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.34
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.53
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.61
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.3
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.21
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.57
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.7
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.36
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.59
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.82
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.73
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.45
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.47
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.43
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.69
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.68
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.48
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.64
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.26
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.2
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.1
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.12
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.19
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154240 p.Met624Ile missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.73
katG 2155413 p.Glu233Asp missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 0.53
PPE35 2169320 p.Leu431Phe missense_variant 0.36
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 0.57
pncA 2289365 c.-125delC upstream_gene_variant 0.53
eis 2714354 p.Gly327Cys missense_variant 0.12
eis 2714357 p.Gly326Cys missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 0.54
ahpC 2726612 c.420C>A synonymous_variant 0.12
thyX 3067515 p.Ser144Ile missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474143 p.Trp46Leu missense_variant 0.22
fprA 3474179 p.Pro58Leu missense_variant 0.2
fprA 3474216 c.210G>A synonymous_variant 0.18
fbiA 3640618 p.Gly26Ser missense_variant 0.17
embC 4240172 p.Val104Met missense_variant 0.6
embC 4240655 p.Ala265Thr missense_variant 0.13
embC 4241089 c.1227C>A synonymous_variant 0.14
embC 4241562 p.Arg567His missense_variant 0.71
embC 4241666 p.Ala602Thr missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.74
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245962 c.-552G>A upstream_gene_variant 0.25
aftB 4267773 p.Ile355Thr missense_variant 0.12
aftB 4267795 p.Ala348Thr missense_variant 0.11
aftB 4268481 p.Pro119Leu missense_variant 0.18
aftB 4268519 c.318C>T synonymous_variant 0.38
ubiA 4269670 p.Val55Gly missense_variant 0.19
ethA 4328329 c.-856C>G upstream_gene_variant 0.32
whiB6 4338213 c.309T>G synonymous_variant 0.1
whiB6 4338217 p.Asn102Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.67
gid 4407742 p.Arg154Gln missense_variant 0.3