TB-Profiler result

Run: SRR7645936
Summary

Run ID: SRR7645936

Sample name:

Date: 04-04-2023 19:59:21

Number of reads: 1271178

Percentage reads mapped: 23.37

Strain: lineage2.2.1

Drug-resistance: Sensitive

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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
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
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 5932 c.694delT frameshift_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7569 p.Ala90Ser missense_variant 0.31
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7592 c.291G>C synonymous_variant 0.22
gyrA 7605 p.Pro102Asp missense_variant 0.24
gyrA 7609 p.Trp103Phe missense_variant 0.25
gyrA 7623 p.Pro108Thr missense_variant 0.17
gyrA 7631 c.330G>C synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491631 c.849C>T synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575815 p.Trp156* stop_gained 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620439 c.553delG frameshift_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620644 p.Glu252Lys missense_variant 0.2
rpoB 760191 p.Val129Ile missense_variant 0.17
rpoC 762899 c.-471G>C upstream_gene_variant 0.35
rpoB 762911 p.Ile1035Met missense_variant 0.43
rpoC 762920 c.-450C>T upstream_gene_variant 0.42
rpoC 762923 c.-447C>G upstream_gene_variant 0.42
rpoC 762929 c.-441G>T upstream_gene_variant 0.44
rpoB 762939 p.Met1045Leu missense_variant 0.42
rpoB 762942 p.Ile1046Val missense_variant 0.44
rpoC 762947 c.-423C>G upstream_gene_variant 0.41
rpoC 762968 c.-402G>A upstream_gene_variant 0.55
rpoC 762971 c.-399G>C upstream_gene_variant 0.48
rpoC 762989 c.-381G>C upstream_gene_variant 0.44
rpoC 762995 c.-375G>T upstream_gene_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764611 c.1242G>T synonymous_variant 0.17
rpoC 764618 c.1249C>T synonymous_variant 0.3
rpoC 764623 c.1254C>G synonymous_variant 0.3
rpoC 764626 c.1257C>T synonymous_variant 0.29
rpoC 764632 c.1263T>C synonymous_variant 0.33
rpoC 764650 c.1281G>T synonymous_variant 0.42
rpoC 764665 c.1296C>G synonymous_variant 0.48
rpoC 764668 c.1299C>T synonymous_variant 0.5
rpoC 764671 c.1302G>A synonymous_variant 0.5
rpoC 764677 c.1308C>G synonymous_variant 0.5
rpoC 764680 c.1311G>A synonymous_variant 0.5
rpoC 764701 c.1332C>G synonymous_variant 0.62
rpoC 764713 c.1344G>T synonymous_variant 0.36
rpoC 764716 c.1347G>C synonymous_variant 0.22
rpoC 764722 c.1353G>T synonymous_variant 0.18
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776864 p.Met539Ile missense_variant 0.13
mmpS5 778750 c.155delA frameshift_variant 0.11
mmpR5 779181 p.Ser64Arg missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781588 p.Lys10Arg missense_variant 0.11
fbiC 1303672 p.Ala248Thr missense_variant 0.12
Rv1258c 1406723 c.618A>G synonymous_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416314 p.Arg345Gln missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.19
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.58
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.77
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.82
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.87
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.87
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.85
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.85
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.85
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.8
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.79
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.78
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.78
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.64
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.17
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.17
rrs 1472328 n.483G>A non_coding_transcript_exon_variant 0.24
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.25
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.32
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.37
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.35
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.31
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.35
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.33
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.62
rrs 1472709 n.864T>G non_coding_transcript_exon_variant 0.61
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.66
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.66
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.85
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.84
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.84
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.87
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.89
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.89
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.89
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.77
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.17
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.2
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.19
rrs 1473075 n.1230A>G non_coding_transcript_exon_variant 0.12
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.34
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.46
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.46
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.62
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.62
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.62
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.63
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.72
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.76
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.8
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 1.0
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.35
rrl 1473602 n.-56G>A upstream_gene_variant 0.12
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.18
rrl 1474221 n.564T>C non_coding_transcript_exon_variant 0.22
rrl 1474228 n.571T>A non_coding_transcript_exon_variant 0.21
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.23
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.25
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.23
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.35
rrl 1474494 n.837C>G non_coding_transcript_exon_variant 0.35
rrl 1474495 n.838G>T non_coding_transcript_exon_variant 0.35
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.35
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.41
rrl 1474503 n.846G>C non_coding_transcript_exon_variant 0.33
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.38
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.38
rrl 1474509 n.852G>C non_coding_transcript_exon_variant 0.44
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.56
rrl 1474528 n.871T>A non_coding_transcript_exon_variant 0.71
rrl 1474530 n.873G>T non_coding_transcript_exon_variant 0.71
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.69
rrl 1474539 n.882C>A non_coding_transcript_exon_variant 0.69
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.69
rrl 1474573 n.916C>T non_coding_transcript_exon_variant 0.74
rrl 1474576 n.919T>A non_coding_transcript_exon_variant 0.68
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.68
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 0.65
rrl 1474586 n.929T>A non_coding_transcript_exon_variant 0.63
rrl 1474587 n.930G>A non_coding_transcript_exon_variant 0.63
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.57
rrl 1474608 n.951T>A non_coding_transcript_exon_variant 0.48
rrl 1474609 n.952G>C non_coding_transcript_exon_variant 0.42
rrl 1474610 n.953C>T non_coding_transcript_exon_variant 0.42
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.16
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.19
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.27
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.27
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.31
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.37
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.76
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.77
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.86
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.86
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.85
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.85
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.88
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.9
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.9
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.9
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.85
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.84
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.79
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.78
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.8
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.81
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.8
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.77
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.57
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.54
fabG1 1673648 p.Arg70His missense_variant 0.14
rpsA 1833683 c.145delG frameshift_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917866 c.-74C>T upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918081 p.Asp48Asn missense_variant 0.14
tlyA 1918353 c.414C>T synonymous_variant 0.11
ndh 2102397 p.Ala216Thr missense_variant 0.11
katG 2154696 c.1416A>T synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155563 c.549C>T synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289776 c.-535C>T upstream_gene_variant 0.14
pepQ 2859957 c.462G>T synonymous_variant 0.11
Rv2752c 3064731 p.Leu487Phe missense_variant 1.0
thyX 3067512 c.433delG frameshift_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641324 p.Ser261Leu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242701 p.Ala947Thr missense_variant 0.14
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244812 p.Cys527Tyr missense_variant 0.22
embA 4246452 p.Val1074Ile missense_variant 0.17
embB 4247163 p.Leu217Pro missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326699 p.Arg259Cys missense_variant 0.12
ethR 4327093 c.-456G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.95