TB-Profiler result

Run: SRR16295791
Summary

Run ID: SRR16295791

Sample name:

Date: 03-04-2023 17:03:16

Number of reads: 3876546

Percentage reads mapped: 59.8

Strain: lineage2.2.1

Drug-resistance: Other

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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 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.56 streptomycin
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 5320 c.81C>T synonymous_variant 0.14
gyrB 5928 p.Pro230Leu missense_variant 0.15
gyrB 5943 p.Glu235Gly missense_variant 0.17
gyrB 7122 p.Pro628Leu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9699 p.Gly800Cys missense_variant 0.17
fgd1 491200 p.Arg140Trp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.57
mshA 576513 p.Leu389Gln missense_variant 0.22
ccsA 619717 c.-174G>A upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763299 p.Ser1165Pro missense_variant 0.17
rpoC 765258 p.Arg630Gln missense_variant 0.17
rpoC 767209 c.3840T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776011 p.Gln824* stop_gained 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776402 c.2079C>A synonymous_variant 0.12
mmpL5 777291 p.Ala397Val missense_variant 0.18
mmpL5 777398 c.1083G>A synonymous_variant 0.12
mmpL5 777639 p.Leu281Pro missense_variant 0.18
mmpR5 779004 c.19delG frameshift_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781732 p.Thr58Met missense_variant 0.12
rpsL 781879 p.Val107Ala missense_variant 0.14
fbiC 1302873 c.-58A>G upstream_gene_variant 0.11
fbiC 1303296 c.366T>C synonymous_variant 0.17
fbiC 1304428 p.Arg500* stop_gained 0.17
fbiC 1305022 p.His698Tyr missense_variant 0.12
Rv1258c 1406357 p.Ile328Met missense_variant 0.22
Rv1258c 1406536 p.Gly269Ser missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416659 p.Arg230Leu missense_variant 0.15
embR 1417313 p.Asp12Gly missense_variant 0.12
embR 1417394 c.-47C>T upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472501 n.656G>A non_coding_transcript_exon_variant 0.12
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.22
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.4
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.4
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.37
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.39
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.39
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.39
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.35
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.37
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.34
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.35
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.39
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.39
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.59
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.62
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.61
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.61
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.64
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.58
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.58
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.58
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.52
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.5
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.5
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.52
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.52
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.12
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrs 1472952 n.1108_1112delGTCTC non_coding_transcript_exon_variant 0.21
rrs 1472959 n.1114_1115insTGTTA non_coding_transcript_exon_variant 0.23
rrs 1472967 n.1122G>T non_coding_transcript_exon_variant 0.2
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.2
rrs 1472971 n.1126G>T non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1129_1130delAT non_coding_transcript_exon_variant 0.21
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.2
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.21
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.21
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.21
rrs 1472990 n.1145A>C non_coding_transcript_exon_variant 0.21
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.21
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.21
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.2
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.2
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.14
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.2
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.2
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.13
rrl 1475239 n.1582A>G non_coding_transcript_exon_variant 0.11
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.17
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.21
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.33
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.33
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.31
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.31
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.31
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.31
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.31
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.31
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.34
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.32
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.33
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.33
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.33
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.5
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.57
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.58
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.58
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.58
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.58
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.57
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.5
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.48
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.48
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.45
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.48
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.45
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.45
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.42
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.42
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.44
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.71
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.71
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.76
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.79
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.79
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.79
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.86
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.85
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.85
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.94
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.91
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.86
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.85
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.84
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.83
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.83
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.8
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.8
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.8
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.8
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.78
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.69
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.67
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.67
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.63
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.62
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.52
rrl 1476602 n.2945G>A non_coding_transcript_exon_variant 0.41
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.24
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.17
rrl 1476712 n.3055C>T non_coding_transcript_exon_variant 0.12
rrl 1476793 n.3136A>G splice_region_variant&non_coding_transcript_exon_variant 0.13
fabG1 1673358 c.-82T>C upstream_gene_variant 0.2
rpsA 1833641 p.Asn34Asp missense_variant 0.18
rpsA 1833648 p.Gly36Val missense_variant 0.17
rpsA 1833651 p.Asp37Ala missense_variant 0.17
rpsA 1833658 c.117C>T synonymous_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834310 p.Glu257Lys missense_variant 0.12
tlyA 1917953 p.Ala5Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156276 c.-165C>T upstream_gene_variant 0.17
PPE35 2167824 p.Gly930Asp missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169970 p.Gly215Ser missense_variant 0.17
PPE35 2170035 p.Val193Ala missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2222913 c.252C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289164 c.78G>A synonymous_variant 0.14
pncA 2289545 c.-304T>C upstream_gene_variant 0.15
pncA 2289762 c.-521G>A upstream_gene_variant 0.2
pncA 2290067 c.-826C>A upstream_gene_variant 0.25
kasA 2518153 c.39C>T synonymous_variant 0.14
kasA 2518348 c.234A>T synonymous_variant 0.17
kasA 2518611 p.Thr166Asn missense_variant 0.13
eis 2714605 c.727delG frameshift_variant 0.25
eis 2715327 c.6T>A synonymous_variant 0.12
eis 2715467 c.-135A>G upstream_gene_variant 1.0
ahpC 2726071 c.-122C>T upstream_gene_variant 0.12
folC 2746413 p.Pro396Ser missense_variant 0.14
folC 2746911 p.Thr230Ala missense_variant 0.15
folC 2747026 c.573C>A synonymous_variant 0.18
pepQ 2859548 p.Gly291Cys missense_variant 0.12
Rv2752c 3065324 p.Ala290Thr missense_variant 0.17
thyX 3067510 c.436C>T synonymous_variant 0.15
thyX 3067630 p.Gln106Lys missense_variant 0.12
thyA 3073888 p.Ser195* stop_gained 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.18
fbiD 3339311 p.Asp65Ala missense_variant 0.12
fbiD 3339314 p.Glu66Ala missense_variant 0.12
fbiD 3339321 c.204G>C synonymous_variant 0.12
fbiD 3339756 p.His213Gln missense_variant 0.2
Rv3083 3449013 c.510C>T synonymous_variant 0.17
Rv3083 3449017 p.Asp172Tyr missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568819 c.-140C>T upstream_gene_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640458 c.-85T>G upstream_gene_variant 0.22
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
fbiB 3641109 c.-426C>T upstream_gene_variant 0.13
fbiB 3641706 p.Gly58Cys missense_variant 0.18
fbiB 3642231 c.697C>T synonymous_variant 0.12
fbiB 3642838 p.Leu435Ser missense_variant 0.13
alr 3840548 c.873G>A synonymous_variant 0.17
rpoA 3878258 p.Val84Leu missense_variant 0.11
rpoA 3878569 c.-62C>G upstream_gene_variant 0.33
ddn 3986925 p.Met28Val missense_variant 0.25
clpC1 4039753 p.Gln318* stop_gained 0.17
clpC1 4040831 c.-128delG upstream_gene_variant 0.17
embC 4240291 c.429G>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246028 c.-486G>T upstream_gene_variant 0.12
embA 4246029 p.Pro933Ser missense_variant 0.12
embB 4247028 p.Leu172Arg missense_variant 0.53
embB 4248008 p.Leu499Met missense_variant 0.17
aftB 4267187 c.1650T>A synonymous_variant 0.18
aftB 4267190 c.1647T>A synonymous_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268250 p.Ala196Val missense_variant 0.2
aftB 4269471 c.-635C>A upstream_gene_variant 0.13
ubiA 4269578 c.255delC frameshift_variant 0.2
ethA 4326474 p.Pro334Ala missense_variant 1.0
whiB6 4338208 p.Pro105Leu missense_variant 0.2
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