TB-Profiler result

Run: SRR3675252
Summary

Run ID: SRR3675252

Sample name:

Date: 04-04-2023 05:24:18

Number of reads: 497722

Percentage reads mapped: 92.23

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
rpoB 761090 p.Ser428Arg missense_variant 0.17 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.26 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.16 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6529 c.-773G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7894 p.Ala198Val missense_variant 0.15
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8657 c.1356C>T synonymous_variant 0.12
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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765649 p.Phe760Leu missense_variant 0.2
rpoC 766691 p.Gly1108Cys missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776045 c.2436G>T synonymous_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406294 c.1047C>A synonymous_variant 0.17
Rv1258c 1406503 p.Val280Leu missense_variant 1.0
embR 1416443 p.Pro302Gln missense_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461087 p.Leu15Met missense_variant 0.15
atpE 1461090 p.Ile16Val missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.23
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.23
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.23
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.18
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.25
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.11
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.28
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.28
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.22
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.22
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.13
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.19
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.19
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.19
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.13
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.23
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.25
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.19
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.19
rrs 1473291 n.1446G>C non_coding_transcript_exon_variant 0.12
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.12
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.14
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.19
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.17
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.13
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.15
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.13
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.13
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.13
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.13
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.16
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.13
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.12
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.12
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.16
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.27
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.22
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.16
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.33
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.23
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.17
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.47
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.19
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.2
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.1
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.14
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.13
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.24
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.11
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.32
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.34
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.32
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.28
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.38
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.17
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.36
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.11
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.13
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.13
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.21
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.22
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.14
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
inhA 1674325 p.Asp42Asn missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154673 p.Ala480Val missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154887 p.Ala409Ser missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168991 p.Ala541Val missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2222089 p.Leu359Ser missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290135 c.-894C>A upstream_gene_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714803 p.Ala177Glu missense_variant 0.17
eis 2715235 p.Ala33Glu missense_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.4
folC 2746896 p.Gly235Trp missense_variant 0.22
folC 2747639 c.-41C>A upstream_gene_variant 0.17
ribD 2987168 c.330C>A synonymous_variant 0.13
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3068138 c.-193C>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338919 c.-199C>A upstream_gene_variant 0.12
fbiD 3339273 c.156T>G synonymous_variant 0.33
fbiD 3339712 p.Arg199Cys missense_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612401 p.Ser239Leu missense_variant 0.13
Rv3236c 3612879 p.Thr80Ala missense_variant 0.17
rpoA 3878200 p.Gly103Asp missense_variant 0.17
rpoA 3878238 p.Asp90Glu missense_variant 0.29
clpC1 4038679 p.Pro676Thr missense_variant 0.12
clpC1 4038899 c.1806C>A synonymous_variant 0.2
clpC1 4040306 c.399G>A synonymous_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239835 c.-28C>A upstream_gene_variant 0.29
embC 4240318 c.456T>C synonymous_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243115 p.Leu1085Met missense_variant 0.2
embC 4243119 p.Trp1086* stop_gained 0.18
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244073 p.Ala281Ser missense_variant 0.13
embA 4244555 p.Gln441His missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.83
aftB 4268156 c.681C>T synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4270023 c.-190G>T upstream_gene_variant 0.17
whiB6 4338224 c.297delC frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>A 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 4407713 p.Gly164Cys missense_variant 0.17
gid 4407873 c.330G>T synonymous_variant 1.0