TB-Profiler result

Run: ERR245662
Summary

Run ID: ERR245662

Sample name:

Date: 31-03-2023 18:13:22

Number of reads: 8698722

Percentage reads mapped: 65.12

Strain: lineage1.2.2.1

Drug-resistance: Sensitive

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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 Indo-Oceanic NA 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
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_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
gyrA 9780 p.Ala827Thr missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576614 c.1267C>A synonymous_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.25
ccsA 620659 p.Arg257Cys missense_variant 0.99
ccsA 620748 c.858T>G synonymous_variant 0.19
rpoB 759831 p.Thr9Pro missense_variant 0.26
rpoB 762249 p.Leu815Val missense_variant 0.19
rpoC 762836 c.-534C>G upstream_gene_variant 0.18
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 764725 p.Phe452Leu missense_variant 0.19
rpoC 767305 p.Tyr1312* stop_gained 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 777399 p.Thr361Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.16
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.17
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.24
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.27
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.27
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.29
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.21
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.17
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.17
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.17
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.16
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.12
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.15
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.21
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.21
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.2
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.21
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.25
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.28
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.34
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.35
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.35
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.36
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.28
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.2
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.2
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.2
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.19
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.19
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.2
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.11
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.17
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.18
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.12
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.13
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.31
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.14
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.13
rrl 1474201 n.544T>G non_coding_transcript_exon_variant 0.14
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.13
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.2
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.2
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.17
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.17
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.19
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.16
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.19
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.21
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.27
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.25
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.18
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.17
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.16
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.17
rrl 1475672 n.2015C>G non_coding_transcript_exon_variant 0.15
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.15
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.23
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.26
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.25
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.25
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.22
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.22
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.29
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.28
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.24
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.23
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.22
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.26
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.31
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.41
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.47
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.48
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.71
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.65
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.64
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.48
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.16
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.17
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.18
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.17
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.17
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.23
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.29
rrl 1476602 n.2945G>A non_coding_transcript_exon_variant 0.3
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.23
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.18
rrl 1476621 n.2964C>A non_coding_transcript_exon_variant 0.17
rrl 1476624 n.2967T>A non_coding_transcript_exon_variant 0.17
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.17
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.17
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.16
rpsA 1834255 c.714C>T synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.23
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.26
ahpC 2725954 c.-239C>T upstream_gene_variant 0.21
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746186 c.1413G>C synonymous_variant 0.26
Rv2752c 3064741 p.Gly484Ala missense_variant 0.22
thyA 3073817 p.Gln219Glu missense_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.3
Rv3083 3449673 p.Tyr390* stop_gained 0.22
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
fprA 3475280 p.Val425Gly missense_variant 0.24
Rv3236c 3611982 p.Ala379Pro missense_variant 0.49
fbiB 3641955 p.Gly141Arg missense_variant 0.28
alr 3841048 c.373C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.19
clpC1 4039932 p.Gly258Val missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.32
embC 4241128 c.1266G>C synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.38
embC 4242827 p.Leu989Val missense_variant 0.23
embA 4245969 p.Pro913Ser missense_variant 0.99
embB 4247041 c.528C>T synonymous_variant 0.24
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249504 p.Gln997His missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 0.99
ubiA 4269529 p.Ala102Gly missense_variant 0.18
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327450 c.-99G>A upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.33
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