TB-Profiler result

Run: SRR12882669
Summary

Run ID: SRR12882669

Sample name:

Date: 03-04-2023 07:53:04

Number of reads: 1060165

Percentage reads mapped: 22.38

Strain: lineage3.1.1

Drug-resistance: RR-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
lineage3 East-African-Indian CAS RD750 0.98
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.92
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.96
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 761116 p.Asn437Thr missense_variant 0.11 rifampicin
rpoB 761127 p.Ser441Ala missense_variant 0.12 rifampicin
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 7585 p.Ser95Thr missense_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.96
rpoB 761133 c.1327T>C synonymous_variant 0.11
rpoB 761156 c.1350G>C synonymous_variant 0.11
rpoB 761162 c.1356G>C synonymous_variant 0.12
rpoB 761165 c.1359G>T synonymous_variant 0.12
rpoB 761171 c.1365C>T synonymous_variant 0.12
rpoB 761178 p.Ser458Thr missense_variant 0.13
rpoB 761183 c.1377T>C synonymous_variant 0.12
rpoB 761189 c.1383T>G synonymous_variant 0.11
rpoB 761198 c.1392G>C synonymous_variant 0.11
rpoB 761204 c.1398C>G synonymous_variant 0.11
rpoB 761219 c.1413G>C synonymous_variant 0.11
rpoB 761222 c.1416G>C synonymous_variant 0.11
rpoB 761348 c.1542C>T synonymous_variant 0.15
rpoB 761408 c.1602G>T synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763550 p.Tyr61His missense_variant 0.11
rpoC 763570 c.201G>C synonymous_variant 0.12
rpoC 763573 c.204G>T synonymous_variant 0.12
rpoC 763586 p.Ile73Val missense_variant 0.11
rpoC 763648 c.279C>G synonymous_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.11
rpoC 763666 c.297G>C synonymous_variant 0.12
rpoC 764605 c.1236G>T synonymous_variant 0.16
rpoC 764611 c.1242G>C synonymous_variant 0.17
rpoC 764614 c.1245G>A synonymous_variant 0.17
rpoC 764623 c.1254C>G synonymous_variant 0.15
rpoC 764626 c.1257C>T synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.16
rpoC 764635 c.1266C>G synonymous_variant 0.16
rpoC 764644 c.1275G>C synonymous_variant 0.17
rpoC 764650 c.1281G>T synonymous_variant 0.17
rpoC 764653 c.1284G>C synonymous_variant 0.17
rpoC 764656 c.1287C>A synonymous_variant 0.17
rpoC 764662 c.1293G>C synonymous_variant 0.17
rpoC 764668 c.1299C>A synonymous_variant 0.19
rpoC 764672 p.Gln435Asn missense_variant 0.21
rpoC 764677 c.1308C>G synonymous_variant 0.2
rpoC 764681 p.Leu438Met missense_variant 0.2
rpoC 764684 p.His439Tyr missense_variant 0.21
rpoC 764701 c.1332C>G synonymous_variant 0.18
rpoC 764705 p.Leu446Glu missense_variant 0.19
rpoC 764719 c.1350G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.15
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.39
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.66
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.63
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.62
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.65
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.64
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.59
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.55
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.55
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.55
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.53
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.5
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.46
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.24
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.51
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.51
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.51
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.52
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.52
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.53
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.51
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.51
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.51
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.53
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.6
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.72
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.71
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.7
rrs 1472669 n.824_825insTGG non_coding_transcript_exon_variant 0.62
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.62
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.62
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.63
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.65
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.64
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.65
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.64
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.66
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.66
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.65
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.66
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.26
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.21
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.65
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.67
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.68
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.68
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.69
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.68
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.68
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.68
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.66
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.69
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.68
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.69
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.7
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.7
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.7
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.7
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.7
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.69
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.69
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.62
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.61
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.53
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.39
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.12
rrl 1474758 n.1101G>A non_coding_transcript_exon_variant 0.19
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.24
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.24
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.24
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.24
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.25
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.24
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.24
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.24
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.23
rrl 1474816 n.1159G>C non_coding_transcript_exon_variant 0.23
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.24
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.24
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.24
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.24
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.26
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.24
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.24
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.24
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.14
rrl 1475108 n.1451C>G non_coding_transcript_exon_variant 0.14
rrl 1475109 n.1452C>A non_coding_transcript_exon_variant 0.14
rrl 1475115 n.1458A>C non_coding_transcript_exon_variant 0.14
rrl 1475154 n.1497C>A non_coding_transcript_exon_variant 0.15
rrl 1475163 n.1506T>G non_coding_transcript_exon_variant 0.11
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.23
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.38
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.54
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.63
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.65
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.62
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.6
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.6
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.61
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.6
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.6
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.6
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.59
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.61
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.62
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.7
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.73
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.81
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.84
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.83
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.76
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.76
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.76
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.76
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.76
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.78
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.78
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.77
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.77
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.78
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.86
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.87
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.89
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.9
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.9
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.9
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.89
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.87
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.9
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.92
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.9
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.88
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.88
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.86
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.87
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.87
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.87
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.87
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.86
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.85
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.85
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.84
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.84
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.81
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.8
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.7
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.59
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.49
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.37
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
katG 2156172 c.-61G>C upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 0.94
PPE35 2170461 p.Gly51Glu missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.93
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2715122 p.Val71Leu missense_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987613 c.775T>C stop_lost&splice_region_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.93
fprA 3474877 p.Arg291Ser missense_variant 0.97
fbiB 3641545 p.Pro4His missense_variant 0.12
fbiB 3642130 p.Ala199Asp missense_variant 0.13
rpoA 3878567 c.-60C>G upstream_gene_variant 0.22
embC 4241562 p.Arg567His missense_variant 0.96
embC 4242075 p.Arg738Gln missense_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246567 c.54G>T synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.93