TB-Profiler result

Run: ERR4815795
Summary

Run ID: ERR4815795

Sample name:

Date: 01-04-2023 14:04:14

Number of reads: 790476

Percentage reads mapped: 77.59

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.98
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 0.89 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575883 p.Thr179Lys missense_variant 0.18
mshA 575946 p.Thr200Met missense_variant 0.12
ccsA 620748 c.858T>G synonymous_variant 0.29
rpoB 759620 c.-187A>C upstream_gene_variant 0.43
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763831 p.Glu154Asp missense_variant 0.11
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 0.94
rpoC 765240 p.Arg624His missense_variant 0.15
rpoC 765707 p.Glu780Lys missense_variant 0.18
rpoC 765723 p.Val785Asp missense_variant 0.13
rpoC 765828 p.Met820Thr missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 777569 c.912C>A synonymous_variant 0.11
mmpL5 778209 p.Ala91Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304106 c.1176G>T synonymous_variant 0.14
fbiC 1304419 p.Ala497Thr missense_variant 1.0
fbiC 1304839 p.Glu637* stop_gained 0.67
embR 1416903 p.Val149Leu missense_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471997 n.152T>C non_coding_transcript_exon_variant 0.33
rrs 1472023 n.178G>C non_coding_transcript_exon_variant 0.5
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.93
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.94
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.94
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.95
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.97
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.97
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.97
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.95
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.98
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.96
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.99
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.98
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.98
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.32
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.95
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.95
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.97
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.88
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.94
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.94
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.89
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.96
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.93
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.92
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.85
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.71
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.71
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.33
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.43
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.57
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.57
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.78
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.6
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.7
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.2
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.75
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.17
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.17
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.23
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.75
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.83
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.75
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.25
rrs 1473070 n.1225G>C non_coding_transcript_exon_variant 0.17
rrs 1473071 n.1226C>A non_coding_transcript_exon_variant 0.14
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.17
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.9
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.86
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.83
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.83
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.83
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.83
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.83
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.83
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.83
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.62
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.67
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.14
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.38
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.44
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.41
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.39
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.12
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.5
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.73
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.73
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.81
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.73
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.81
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.73
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.83
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.82
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.81
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.74
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.74
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.71
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.71
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.65
rrl 1473484 n.-173delA upstream_gene_variant 0.5
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0
rrl 1474628 n.971C>T non_coding_transcript_exon_variant 0.67
rrl 1474635 n.979_982delACCG non_coding_transcript_exon_variant 1.0
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.89
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.91
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.91
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.67
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
rrl 1476694 n.3037G>A non_coding_transcript_exon_variant 0.22
inhA 1674730 p.Arg177Cys missense_variant 0.15
rpsA 1833695 c.155delT frameshift_variant 0.1
tlyA 1917830 c.-110C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101948 c.1095C>T synonymous_variant 0.17
ndh 2102498 p.Gly182Val missense_variant 0.15
katG 2154655 p.Ser486Asn missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155099 p.Gly338Asp missense_variant 0.14
PPE35 2167735 p.Pro960Ser missense_variant 0.14
PPE35 2167859 c.2754T>C synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168930 c.1682delC frameshift_variant 0.14
PPE35 2170096 c.517C>A synonymous_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290136 c.-895C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518809 p.Lys232Arg missense_variant 0.12
kasA 2518839 p.Ala242Gly missense_variant 0.1
kasA 2519217 p.Pro368Leu missense_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.5
ribD 2986674 c.-165G>T upstream_gene_variant 0.17
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065317 p.Ala292Val missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474144 p.Trp46Cys missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568771 c.-92C>G upstream_gene_variant 0.14
fbiA 3640398 c.-145G>C upstream_gene_variant 1.0
fbiA 3640593 c.55delG frameshift_variant 0.11
fbiB 3641735 c.201C>A synonymous_variant 0.12
clpC1 4038428 c.2277G>A synonymous_variant 0.13
clpC1 4038692 c.2013C>T synonymous_variant 0.13
clpC1 4039829 p.Leu292Phe missense_variant 0.11
clpC1 4040306 c.399G>A synonymous_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044274 p.Arg3Leu missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242274 c.-959G>A upstream_gene_variant 0.12
embC 4242581 p.Ala907Thr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244525 c.1293G>T synonymous_variant 0.11
embA 4245218 c.1986C>T synonymous_variant 1.0
embA 4245496 p.Gly755Val missense_variant 0.11
embB 4245629 c.-885C>T upstream_gene_variant 0.4
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246594 c.81C>T synonymous_variant 0.11
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249681 c.3168C>T synonymous_variant 0.13
aftB 4268560 c.277C>T synonymous_variant 0.14
ubiA 4269031 p.Gly268Asp missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327777 p.Asp77Asn missense_variant 0.11
whiB6 4338536 c.-15G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0