TB-Profiler result

Run: SRR1140627
Summary

Run ID: SRR1140627

Sample name:

Date: 02-04-2023 20:56:58

Number of reads: 623418

Percentage reads mapped: 19.81

Strain: lineage4.6.1

Drug-resistance: Other

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
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 1918634 p.Gly232Asp missense_variant 0.13 capreomycin
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
gyrB 5188 c.-52C>A upstream_gene_variant 0.12
gyrB 5537 p.Met100Leu missense_variant 0.13
gyrB 6020 p.Val261Met missense_variant 0.13
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 7629 p.Val110Met missense_variant 0.18
gyrA 7881 p.Leu194Met missense_variant 0.18
gyrA 8621 p.Leu440Phe missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9435 p.Leu712Met missense_variant 0.14
fgd1 491321 p.Ala180Val missense_variant 0.25
mshA 575242 c.-106G>T upstream_gene_variant 0.22
mshA 575283 c.-65C>A upstream_gene_variant 0.29
mshA 576071 p.Val242Ile missense_variant 0.25
ccsA 620057 p.Thr56Ser missense_variant 0.22
ccsA 620198 p.Gln103Arg missense_variant 0.12
ccsA 620309 c.421delC frameshift_variant 0.18
rpoB 760400 c.594G>A synonymous_variant 0.15
rpoB 762461 p.Asn885Lys missense_variant 0.22
rpoC 762899 c.-471G>C upstream_gene_variant 0.33
rpoC 762917 c.-453C>G upstream_gene_variant 0.5
rpoC 762920 c.-450C>T upstream_gene_variant 0.5
rpoC 762923 c.-447C>G upstream_gene_variant 0.5
rpoB 762925 p.Thr1040Ile missense_variant 0.5
rpoB 762939 p.Met1045Leu missense_variant 0.47
rpoB 762942 p.Ile1046Val missense_variant 0.45
rpoC 762962 c.-408C>T upstream_gene_variant 0.54
rpoC 762989 c.-381G>C upstream_gene_variant 0.42
rpoC 762995 c.-375G>T upstream_gene_variant 0.32
rpoC 764093 p.Arg242Cys missense_variant 0.25
rpoC 764566 c.1197C>G synonymous_variant 0.27
rpoC 764575 c.1206T>G synonymous_variant 0.31
rpoC 764581 c.1212T>C synonymous_variant 0.31
rpoC 764582 p.Leu405Met missense_variant 0.31
rpoC 764587 c.1218C>G synonymous_variant 0.36
rpoC 764605 c.1236G>C synonymous_variant 0.52
rpoC 764611 c.1242G>T synonymous_variant 0.52
rpoC 764632 c.1263T>C synonymous_variant 0.71
rpoC 764641 c.1272C>T synonymous_variant 0.69
rpoC 764650 c.1281G>T synonymous_variant 0.6
rpoC 764663 p.Val432Thr missense_variant 0.33
rpoC 764668 c.1299C>T synonymous_variant 0.3
rpoC 764672 p.Gln435Glu missense_variant 0.3
rpoC 764677 c.1308C>G synonymous_variant 0.3
rpoC 764695 c.1326T>C synonymous_variant 0.2
rpoC 765446 p.Gln693* stop_gained 0.13
rpoC 766297 c.2928G>T synonymous_variant 0.33
rpoC 767161 c.3792C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776847 p.Gln545Arg missense_variant 0.22
mmpL5 777579 p.Thr301Asn missense_variant 0.33
mmpL5 777764 c.717G>T synonymous_variant 0.14
mmpL5 778368 p.Gly38Ala missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781525 c.-35A>T upstream_gene_variant 0.14
rplC 801054 c.246G>A synonymous_variant 0.22
fbiC 1303610 p.Gly227Glu missense_variant 0.12
fbiC 1304094 p.Met388Ile missense_variant 0.14
fbiC 1305447 c.2517C>A synonymous_variant 0.13
Rv1258c 1406613 p.Glu243Gly missense_variant 0.14
Rv1258c 1407529 c.-189T>C upstream_gene_variant 0.12
embR 1416364 c.984C>T synonymous_variant 0.17
embR 1416724 p.Trp208Cys missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.23
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.25
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.27
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.53
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.73
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.75
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.72
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 0.68
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.68
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.68
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.68
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.68
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.56
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.25
rrs 1472303 n.458G>C non_coding_transcript_exon_variant 0.25
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.38
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.41
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.47
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.48
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.69
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.72
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.74
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.67
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.5
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.43
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.29
rrs 1472499 n.654A>G non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.35
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.46
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.23
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.45
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.46
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.77
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.86
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.84
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.85
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.79
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.74
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.58
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.53
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.21
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.14
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrs 1473223 n.1378G>A non_coding_transcript_exon_variant 0.19
rrs 1473352 n.1507C>G non_coding_transcript_exon_variant 0.19
rrs 1473353 n.1508C>G non_coding_transcript_exon_variant 0.19
rrs 1473358 n.1513G>C non_coding_transcript_exon_variant 0.19
rrs 1473359 n.1514G>C non_coding_transcript_exon_variant 0.19
rrl 1474922 n.1265G>C non_coding_transcript_exon_variant 0.14
rrl 1475091 n.1434G>T non_coding_transcript_exon_variant 0.13
rrl 1475790 n.2133C>A non_coding_transcript_exon_variant 0.16
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.17
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.42
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.44
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.47
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.46
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.41
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.43
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.14
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 0.17
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.7
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.73
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.71
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.73
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.76
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.83
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.83
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.85
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.87
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.83
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.84
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.83
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.8
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.78
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.72
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.67
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.52
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.45
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.38
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.25
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.18
inhA 1673718 c.-484G>A upstream_gene_variant 0.18
fabG1 1673915 p.Gly159Ala missense_variant 0.13
fabG1 1674143 p.Ala235Val missense_variant 0.22
inhA 1674350 p.Ile50Thr missense_variant 0.12
rpsA 1833374 c.-168C>T upstream_gene_variant 0.12
rpsA 1834024 c.483G>C synonymous_variant 0.4
rpsA 1834435 c.894G>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101788 p.Val419Leu missense_variant 0.14
ndh 2101903 c.1140C>A synonymous_variant 0.25
ndh 2102293 c.750C>T synonymous_variant 0.15
ndh 2103143 c.-101G>T upstream_gene_variant 0.4
katG 2153933 p.Ala727Thr missense_variant 0.25
katG 2154555 c.1557C>A synonymous_variant 0.25
katG 2155265 p.Leu283Met missense_variant 0.5
Rv1979c 2223233 c.-69G>A upstream_gene_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289209 c.33C>T synonymous_variant 0.2
pncA 2289824 c.-583T>A upstream_gene_variant 0.2
kasA 2519048 p.Gly312Ser missense_variant 0.33
eis 2714640 c.693C>T synonymous_variant 0.17
eis 2714890 p.Arg148Leu missense_variant 0.14
ahpC 2726333 p.Trp47Cys missense_variant 0.11
folC 2746250 p.Ala450Asp missense_variant 0.25
folC 2747143 c.456C>T synonymous_variant 0.13
pepQ 2859847 p.Glu191Val missense_variant 0.17
pepQ 2860176 c.243C>A synonymous_variant 0.5
pepQ 2860466 c.-48C>T upstream_gene_variant 0.17
ribD 2987516 c.678C>A synonymous_variant 0.17
Rv2752c 3064654 p.Ala513Val missense_variant 0.29
Rv2752c 3065086 p.Arg369Met missense_variant 0.29
ald 3086744 c.-76A>G upstream_gene_variant 0.18
ald 3087600 p.Gly261Cys missense_variant 0.14
fbiD 3339119 c.2T>C start_lost 0.29
Rv3083 3448480 c.-24G>A upstream_gene_variant 0.22
Rv3083 3448525 c.22C>T synonymous_variant 0.12
Rv3083 3449477 p.Thr325Asn missense_variant 0.17
fprA 3473874 c.-132delG upstream_gene_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474968 p.Ser321Leu missense_variant 0.4
Rv3236c 3612151 c.966G>T synonymous_variant 0.18
Rv3236c 3612499 c.618C>T synonymous_variant 0.22
fbiA 3640745 p.Thr68Ile missense_variant 0.25
fbiA 3640909 p.Tyr123His missense_variant 0.2
fbiA 3640934 p.Ala131Val missense_variant 0.22
alr 3840267 p.Thr385Ile missense_variant 0.18
ddn 3986930 c.87C>T synonymous_variant 0.22
ddn 3986958 p.Gly39Cys missense_variant 0.17
clpC1 4039496 p.Ile403Met missense_variant 0.23
clpC1 4039526 c.1179G>C synonymous_variant 0.21
clpC1 4039533 p.Asn391Thr missense_variant 0.27
clpC1 4039546 p.Asp387Asn missense_variant 0.17
clpC1 4039549 p.Ala386Ser missense_variant 0.17
clpC1 4039640 c.1065C>G synonymous_variant 0.67
clpC1 4039645 p.His354Asp missense_variant 0.67
clpC1 4039661 c.1044T>C synonymous_variant 0.4
clpC1 4039664 c.1041G>C synonymous_variant 0.33
clpC1 4039667 p.Gln346Phe missense_variant 0.29
clpC1 4039673 c.1032G>A synonymous_variant 0.22
clpC1 4039682 c.1023C>G synonymous_variant 0.25
clpC1 4039690 p.Glu339Gln missense_variant 0.33
clpC1 4039691 c.1014G>C synonymous_variant 0.33
clpC1 4039697 c.1008C>G synonymous_variant 0.33
clpC1 4039711 p.Ile332Val missense_variant 0.42
clpC1 4039712 c.993C>T synonymous_variant 0.42
clpC1 4039718 c.987C>T synonymous_variant 0.38
clpC1 4039739 c.966C>G synonymous_variant 0.18
clpC1 4040580 c.124delG frameshift_variant 0.2
embC 4241284 c.1422G>A synonymous_variant 0.18
embC 4241504 p.Val548Leu missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244701 p.Gly490Val missense_variant 0.2
embB 4247673 p.Ala387Glu missense_variant 0.25
embB 4248050 p.Gly513Trp missense_variant 0.25
embB 4248579 p.Ala689Val missense_variant 0.2
embB 4248766 c.2253C>T synonymous_variant 0.15
aftB 4268353 p.Leu162Val missense_variant 0.13
aftB 4269153 c.-317C>T upstream_gene_variant 0.22
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407661 p.Ser181Leu missense_variant 0.15