TB-Profiler result

Run: SRR1062937
Summary

Run ID: SRR1062937

Sample name:

Date: 02-04-2023 18:41:35

Number of reads: 604489

Percentage reads mapped: 20.19

Strain: lineage4.6.1

Drug-resistance: HR-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 1.0
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.99
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
tlyA 1917979 p.Arg14Trp missense_variant 0.13 capreomycin
katG 2154657 c.1454delG frameshift_variant 0.12 isoniazid
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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8060 p.Met253Ile missense_variant 0.18
gyrA 8456 p.Asn385Lys missense_variant 0.13
gyrA 8602 p.Ala434Val missense_variant 0.2
gyrA 9112 p.Pro604His missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9751 c.2451delC frameshift_variant 0.22
fgd1 491173 c.391C>A synonymous_variant 0.15
mshA 576402 p.Ser352Phe missense_variant 0.12
ccsA 619870 c.-20delG upstream_gene_variant 0.15
ccsA 620074 p.Gly62Arg missense_variant 0.14
ccsA 620396 p.Ser169Tyr missense_variant 0.15
rpoB 760996 p.Arg397Gln missense_variant 0.4
rpoB 761162 c.1356G>A synonymous_variant 0.17
rpoB 761634 p.Val610Met missense_variant 0.22
rpoB 761678 p.Met624Ile missense_variant 0.4
rpoB 762141 p.Asp779Asn missense_variant 0.33
rpoC 762887 c.-483G>C upstream_gene_variant 0.23
rpoC 762899 c.-471G>C upstream_gene_variant 0.41
rpoC 762917 c.-453C>G upstream_gene_variant 0.37
rpoC 762920 c.-450C>T upstream_gene_variant 0.35
rpoC 762923 c.-447C>G upstream_gene_variant 0.35
rpoB 762925 p.Thr1040Ile missense_variant 0.37
rpoB 762939 p.Met1045Leu missense_variant 0.33
rpoB 762942 p.Ile1046Val missense_variant 0.33
rpoC 762962 c.-408C>T upstream_gene_variant 0.36
rpoC 762989 c.-381G>C upstream_gene_variant 0.23
rpoC 764566 c.1197C>G synonymous_variant 0.15
rpoC 764575 c.1206T>G synonymous_variant 0.17
rpoC 764581 c.1212T>C synonymous_variant 0.19
rpoC 764582 p.Leu405Met missense_variant 0.19
rpoC 764587 c.1218C>G synonymous_variant 0.28
rpoC 764605 c.1236G>C synonymous_variant 0.56
rpoC 764611 c.1242G>T synonymous_variant 0.61
rpoC 764632 c.1263T>C synonymous_variant 0.58
rpoC 764641 c.1272C>T synonymous_variant 0.6
rpoC 764650 c.1281G>T synonymous_variant 0.55
rpoC 764663 p.Val432Thr missense_variant 0.56
rpoC 764667 p.Gly433Asp missense_variant 0.12
rpoC 764672 p.Gln435Glu missense_variant 0.45
rpoC 764677 c.1308C>G synonymous_variant 0.47
rpoC 764695 c.1326T>C synonymous_variant 0.33
rpoC 764701 c.1332C>G synonymous_variant 0.18
rpoC 766251 p.Lys961Met missense_variant 0.18
rpoC 766267 c.2898G>A synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776150 p.Met777Ile missense_variant 0.17
mmpL5 776222 c.2259A>G synonymous_variant 0.12
mmpL5 776242 p.Lys747* stop_gained 0.12
mmpL5 777530 c.951C>T synonymous_variant 0.2
mmpL5 777796 p.Ser229Pro missense_variant 0.29
mmpL5 779076 c.-596G>A upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801121 p.Ile105Val missense_variant 0.15
Rv1258c 1406569 p.Val258Met missense_variant 0.14
Rv1258c 1406799 p.Phe181Tyr missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.76
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.8
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.76
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.74
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.74
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.74
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.65
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.62
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.57
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.52
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.54
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.37
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.31
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.31
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.31
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.33
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.33
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.32
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.32
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.26
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.31
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.31
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.31
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.38
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.36
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.36
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.66
rrs 1472770 n.925C>T 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 0.63
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.65
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.63
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.57
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.54
rrs 1473110 n.1267delA non_coding_transcript_exon_variant 0.17
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.14
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.12
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.12
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.16
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.15
rrs 1473223 n.1378G>A non_coding_transcript_exon_variant 0.18
rrl 1475790 n.2133C>A non_coding_transcript_exon_variant 0.17
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.24
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 0.52
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.52
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.33
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.35
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.22
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.69
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.78
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.78
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.8
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.8
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.83
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.84
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.88
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.88
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.88
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.86
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.81
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.84
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.81
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.76
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.77
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.64
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.6
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.52
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.38
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.29
fabG1 1673166 c.-274C>A upstream_gene_variant 0.2
fabG1 1674095 p.Gly219Ala missense_variant 0.18
inhA 1674961 p.Thr254Ala missense_variant 0.18
rpsA 1833501 c.-41C>G upstream_gene_variant 0.17
rpsA 1833631 c.90C>T synonymous_variant 0.15
rpsA 1834631 c.1092delA frameshift_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918728 c.789G>A synonymous_variant 0.22
ndh 2102201 p.Ser281Leu missense_variant 0.3
katG 2154054 p.Lys686Asn missense_variant 0.25
katG 2154885 c.1227C>G synonymous_variant 0.33
katG 2155287 c.825C>T synonymous_variant 0.25
katG 2155640 p.Lys158Glu missense_variant 0.22
PPE35 2167737 p.Leu959Gln missense_variant 0.14
PPE35 2169401 c.1212G>A synonymous_variant 0.17
PPE35 2169864 p.Ala250Asp missense_variant 0.17
Rv1979c 2222115 p.Met350Ile missense_variant 0.17
Rv1979c 2223156 c.9C>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289808 c.-567C>T upstream_gene_variant 0.14
pncA 2290072 c.-831T>G upstream_gene_variant 0.15
kasA 2519164 c.1052delG frameshift_variant 0.22
eis 2714167 p.Ala389Val missense_variant 0.12
ahpC 2726150 c.-43G>A upstream_gene_variant 0.14
folC 2747256 p.Ile115Val missense_variant 0.11
pepQ 2860369 p.Ser17Tyr missense_variant 0.15
ribD 2986853 c.15T>C synonymous_variant 0.2
ribD 2986949 p.Asp37Glu missense_variant 0.12
Rv2752c 3065031 c.1161G>C synonymous_variant 0.12
thyA 3073814 p.Leu220Phe missense_variant 0.17
thyA 3074019 c.453G>A synonymous_variant 0.12
thyA 3074295 c.177G>A synonymous_variant 0.2
thyA 3074343 c.129G>A synonymous_variant 0.2
ald 3087571 p.Ser251Leu missense_variant 0.18
ald 3087630 p.Gln271* stop_gained 0.13
ald 3087669 p.Asp284Asn missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474321 c.315C>G synonymous_variant 0.25
fprA 3474573 c.567C>A synonymous_variant 0.14
whiB7 3568732 c.-53C>A upstream_gene_variant 0.18
fbiA 3640453 c.-90C>G upstream_gene_variant 0.12
fbiB 3641952 p.Leu140Ile missense_variant 0.14
fbiB 3642179 c.645G>T synonymous_variant 0.18
clpC1 4038484 p.Gln741* stop_gained 0.22
clpC1 4039175 p.Met510Ile missense_variant 0.18
clpC1 4039258 p.Gln483Lys missense_variant 0.17
clpC1 4039682 c.1023C>G synonymous_variant 0.15
clpC1 4039690 p.Glu339Gln missense_variant 0.16
clpC1 4039691 c.1014G>C synonymous_variant 0.16
clpC1 4039697 c.1008C>G synonymous_variant 0.14
clpC1 4039711 p.Ile332Val missense_variant 0.17
clpC1 4039712 c.993C>T synonymous_variant 0.16
clpC1 4039718 c.987C>T synonymous_variant 0.19
clpC1 4039739 c.966C>G synonymous_variant 0.18
clpC1 4040081 c.624C>A synonymous_variant 0.2
clpC1 4040183 c.522C>T synonymous_variant 0.18
panD 4044397 c.-116G>A upstream_gene_variant 0.15
embC 4239686 c.-177C>T upstream_gene_variant 0.21
embC 4240623 p.Ala254Asp missense_variant 0.12
embC 4240713 p.Trp284Leu missense_variant 0.25
embC 4241126 p.Leu422Met missense_variant 0.25
embC 4241556 p.Ser565Ile missense_variant 0.29
embC 4241608 c.1746C>A synonymous_variant 0.18
embC 4242139 c.2277G>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242799 c.-434T>C upstream_gene_variant 0.12
embC 4242879 p.Thr1006Ile missense_variant 0.25
embA 4245371 p.Tyr713* stop_gained 0.29
embB 4246974 p.His154Arg missense_variant 0.18
embB 4247044 c.531C>G synonymous_variant 0.25
embB 4248370 c.1857G>A synonymous_variant 0.29
embB 4249605 p.Gly1031Ala missense_variant 0.12
aftB 4267569 p.Pro423Gln missense_variant 0.25
aftB 4269270 c.-434G>A upstream_gene_variant 0.22
ethA 4326010 c.1464G>A synonymous_variant 0.14
ethA 4327280 p.Arg65Leu missense_variant 0.25
ethR 4327864 p.Gly106Arg missense_variant 0.33
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407889 p.Val105Gly missense_variant 0.18
gid 4408312 c.-110C>G upstream_gene_variant 0.12