TB-Profiler result

Run: SRR19303931
Summary

Run ID: SRR19303931

Sample name:

Date: 03-04-2023 21:14:16

Number of reads: 583046

Percentage reads mapped: 13.56

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
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 5803 c.564A>G synonymous_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8802 p.Ala501Thr missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575675 p.Arg110Cys missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 762863 c.-507T>G upstream_gene_variant 0.2
rpoB 762872 c.3067_3068delTA frameshift_variant 0.22
rpoC 762887 c.-483G>C upstream_gene_variant 0.15
rpoB 762888 p.His1028Asn missense_variant 0.15
rpoC 762899 c.-471G>C upstream_gene_variant 0.21
rpoB 762911 p.Ile1035Met missense_variant 0.21
rpoC 762917 c.-453C>G upstream_gene_variant 0.25
rpoC 762929 c.-441G>T upstream_gene_variant 0.29
rpoB 762939 p.Met1045Leu missense_variant 0.27
rpoB 762942 p.Ile1046Val missense_variant 0.29
rpoC 762965 c.-405T>C upstream_gene_variant 0.36
rpoC 762971 c.-399G>T upstream_gene_variant 0.25
rpoC 762980 c.-390T>C upstream_gene_variant 0.27
rpoC 762989 c.-381G>C upstream_gene_variant 0.2
rpoC 762995 c.-375G>C upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764521 c.1152T>C synonymous_variant 0.29
rpoC 764536 c.1167G>C synonymous_variant 0.29
rpoC 764537 p.Pro390Val missense_variant 0.29
rpoC 764540 p.Val391Ile missense_variant 0.29
rpoC 764548 c.1179G>C synonymous_variant 0.25
rpoC 764549 p.Pro394Ala missense_variant 0.25
rpoC 764552 p.Gly395Asn missense_variant 0.29
rpoC 764557 p.Asn396Lys missense_variant 0.29
rpoC 764566 c.1197C>G synonymous_variant 0.29
rpoC 764575 c.1206T>C synonymous_variant 0.29
rpoC 764576 p.Ser403Ala missense_variant 0.29
rpoC 764581 c.1212T>C synonymous_variant 0.25
rpoC 764582 p.Leu405Met missense_variant 0.29
rpoC 764585 p.Leu406Ile missense_variant 0.47
rpoC 764605 c.1236G>C synonymous_variant 0.7
rpoC 764611 c.1242G>C synonymous_variant 0.73
rpoC 764632 c.1263T>C synonymous_variant 0.62
rpoC 764635 c.1266C>G synonymous_variant 0.5
rpoC 764638 c.1269C>T synonymous_variant 0.5
rpoC 764644 c.1275G>C synonymous_variant 0.58
rpoC 764650 c.1281G>A synonymous_variant 0.59
rpoC 764656 c.1287C>G synonymous_variant 0.54
rpoC 764668 c.1299C>T synonymous_variant 0.54
rpoC 764676 p.Leu436Arg missense_variant 0.46
rpoC 764677 c.1309_1311delAAG conservative_inframe_deletion 0.5
rpoC 764705 p.Leu446Lys missense_variant 0.52
rpoC 764719 c.1350G>A synonymous_variant 0.48
rpoC 764858 c.1489T>C synonymous_variant 0.15
rpoC 764869 c.1500C>T synonymous_variant 0.14
rpoC 764872 c.1503A>G synonymous_variant 0.14
rpoC 764875 c.1506C>G synonymous_variant 0.15
rpoC 764887 c.1518G>C synonymous_variant 0.14
rpoC 764888 c.1519_1521delTTGinsCTC synonymous_variant 0.15
rpoC 764902 c.1533C>G synonymous_variant 0.16
rpoC 764911 c.1542A>G synonymous_variant 0.16
rpoC 764913 p.Met515Lys missense_variant 0.16
rpoC 764917 c.1548G>C synonymous_variant 0.15
rpoC 764918 p.Val517Ile missense_variant 0.15
rpoC 764932 c.1563C>G synonymous_variant 0.18
rpoC 764935 c.1566T>C synonymous_variant 0.18
rpoC 764948 c.1579_1581delTTGinsCTC synonymous_variant 0.19
rpoC 764953 c.1584G>C synonymous_variant 0.19
rpoC 764957 p.Glu530Thr missense_variant 0.19
rpoC 764962 c.1593G>A synonymous_variant 0.19
rpoC 764968 c.1599T>C synonymous_variant 0.22
rpoC 764983 c.1614T>C synonymous_variant 0.2
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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302751 c.-180G>A upstream_gene_variant 0.13
fbiC 1303845 c.915C>T synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471778 n.-68G>A upstream_gene_variant 0.18
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.17
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.14
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.35
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.28
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.48
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.48
rrs 1472130 n.285G>C non_coding_transcript_exon_variant 0.39
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.48
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.48
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.46
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.46
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.46
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.44
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.46
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.44
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.46
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.35
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.35
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.29
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.14
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.14
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.14
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.57
rrs 1472517 n.672T>C non_coding_transcript_exon_variant 0.6
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.17
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.73
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.8
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.6
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.2
rrs 1472545 n.700A>G non_coding_transcript_exon_variant 0.75
rrs 1472555 n.710C>T non_coding_transcript_exon_variant 0.55
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.55
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.27
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.82
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.55
rrs 1472573 n.728C>A non_coding_transcript_exon_variant 0.55
rrs 1472596 n.751G>A non_coding_transcript_exon_variant 0.55
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.73
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.67
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.64
rrs 1472648 n.803G>C non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.38
rrs 1472694 n.849C>T non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.5
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.5
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>G non_coding_transcript_exon_variant 0.5
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.6
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.6
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.59
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.62
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.46
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.25
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.52
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.9
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.9
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.87
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.87
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.86
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.9
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.88
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.91
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.89
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.88
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.88
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.87
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.87
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.9
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.87
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.86
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.84
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.76
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.76
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.64
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.63
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.22
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.36
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.21
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.32
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.22
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.25
rrs 1473200 n.1355A>T non_coding_transcript_exon_variant 0.23
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.27
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.27
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.14
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.14
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.14
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.13
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.14
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.18
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.21
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.23
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.21
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.21
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.23
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.23
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.23
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.21
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.21
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.19
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.19
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.2
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.19
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.25
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.15
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.14
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.14
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.14
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.14
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.5
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.53
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.53
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.61
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.67
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.46
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.73
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.47
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.63
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.74
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.75
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.48
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.21
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.52
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.49
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.63
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.62
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.48
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.7
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.73
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.51
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.15
rrl 1476711 n.3054G>A non_coding_transcript_exon_variant 0.2
fabG1 1674160 p.Gly241Ser missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168639 c.1974T>A synonymous_variant 0.14
PPE35 2169219 p.Leu465Pro missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289496 c.-255G>A upstream_gene_variant 0.14
folC 2747559 p.Ala14Thr missense_variant 0.13
pepQ 2859586 p.Arg278His missense_variant 0.13
Rv2752c 3064731 p.Leu487Phe missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612208 c.909G>A synonymous_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641125 p.Ala195Thr missense_variant 0.12
fbiB 3641705 c.171G>A synonymous_variant 1.0
rpoA 3878265 c.243G>A synonymous_variant 0.17
clpC1 4040045 c.660C>G synonymous_variant 0.29
embC 4240190 p.Pro110Ser missense_variant 0.18
embC 4241945 p.Arg695Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249621 c.3108G>T synonymous_variant 1.0
aftB 4267397 c.1440G>A synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268336 c.501C>T synonymous_variant 0.22
aftB 4268868 c.-32G>T upstream_gene_variant 0.15
ethR 4326574 c.-975G>A upstream_gene_variant 0.13
ethR 4326625 c.-924G>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0