TB-Profiler result

Run: ERR245716
Summary

Run ID: ERR245716

Sample name:

Date: 31-03-2023 18:16:30

Number of reads: 5835997

Percentage reads mapped: 55.47

Strain: lineage2.2.1

Drug-resistance: Sensitive

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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
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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575821 c.474G>C synonymous_variant 0.12
mshA 575824 c.477T>G synonymous_variant 0.19
mshA 575830 c.483C>G synonymous_variant 0.19
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.23
rpoB 760934 c.1128C>T synonymous_variant 0.13
rpoB 761057 c.1251G>C synonymous_variant 0.13
rpoB 761180 c.1374A>C synonymous_variant 0.12
rpoB 761312 c.1506G>C synonymous_variant 0.13
rpoB 762266 c.2460T>C synonymous_variant 0.12
rpoC 762836 c.-534C>G upstream_gene_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763732 c.363C>G synonymous_variant 0.12
rpoC 763741 c.372C>T synonymous_variant 0.12
rpoC 763744 c.375G>C synonymous_variant 0.13
rpoC 763765 c.396T>C synonymous_variant 0.15
rpoC 763774 c.405G>C synonymous_variant 0.15
rpoC 763807 c.438T>C synonymous_variant 0.12
rpoC 763816 c.447C>G synonymous_variant 0.12
rpoC 764521 c.1152T>C synonymous_variant 0.12
rpoC 764593 c.1224C>T synonymous_variant 0.12
rpoC 764809 c.1440C>T synonymous_variant 0.12
rpoC 764815 c.1446A>G synonymous_variant 0.13
rpoC 764827 c.1458G>C synonymous_variant 0.12
rpoC 765383 p.Met672Leu missense_variant 0.15
rpoC 765409 c.2040T>C synonymous_variant 0.14
rpoC 765421 c.2052C>G synonymous_variant 0.13
rpoC 765478 c.2109T>C synonymous_variant 0.16
rpoC 765499 c.2130C>G synonymous_variant 0.13
rpoC 765541 c.2172C>G synonymous_variant 0.13
rpoC 765580 c.2211G>C synonymous_variant 0.14
rpoC 765631 p.Asp754Glu missense_variant 0.12
rpoC 765700 c.2331T>C synonymous_variant 0.17
rpoC 765734 c.2365T>C synonymous_variant 0.14
rpoC 765739 c.2370G>T synonymous_variant 0.12
rpoC 766381 c.3012C>T synonymous_variant 0.14
rpoC 766384 c.3015A>G synonymous_variant 0.13
rpoC 766408 c.3039C>G synonymous_variant 0.15
rpoC 766411 c.3042C>G synonymous_variant 0.15
rpoC 766660 c.3291G>C synonymous_variant 0.12
rpoC 766765 c.3396A>C synonymous_variant 0.14
rpoC 766774 c.3405T>C synonymous_variant 0.14
rpoC 766801 c.3432C>G synonymous_variant 0.15
rpoC 766804 c.3435A>G synonymous_variant 0.13
rpoC 766861 c.3492G>T synonymous_variant 0.12
rpoC 766864 c.3495G>C synonymous_variant 0.12
rpoC 766876 c.3507C>T synonymous_variant 0.16
rpoC 766882 c.3513C>T synonymous_variant 0.13
rpoC 766894 c.3525T>C synonymous_variant 0.14
rpoC 766900 c.3531T>C synonymous_variant 0.13
rpoC 766933 c.3564A>G synonymous_variant 0.13
rpoC 767233 c.3864T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781832 c.273T>C synonymous_variant 0.14
rpsL 781838 c.279G>C synonymous_variant 0.14
rpsL 781841 c.282C>G synonymous_variant 0.14
rpsL 781877 c.318T>C synonymous_variant 0.15
fbiC 1304958 c.2028T>G synonymous_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407522 c.-182C>G upstream_gene_variant 0.21
embR 1417233 c.115C>T synonymous_variant 0.31
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.19
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.21
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.31
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.33
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.35
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.14
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.21
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.26
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.3
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.29
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.23
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.23
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.16
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.21
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.21
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.21
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.25
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.44
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.47
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.47
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.48
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.36
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.13
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.16
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.32
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.31
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.31
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.31
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.29
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.28
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.12
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.18
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.22
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.23
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.23
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.24
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.17
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.13
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.12
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.15
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.14
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.13
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.17
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.16
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.15
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.14
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.16
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.12
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.15
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.15
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.19
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.27
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.22
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.17
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.21
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.15
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.12
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.14
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.14
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.15
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.14
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.13
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.16
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.16
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.17
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.12
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.12
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.12
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.14
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.17
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.17
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.17
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.24
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 0.26
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.24
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.28
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.29
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.38
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.39
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.31
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.3
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.3
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.27
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.4
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.44
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.53
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.54
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.72
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.69
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.68
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.59
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.49
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.26
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.13
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.15
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.2
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.2
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.2
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.35
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.42
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.43
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.38
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.3
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.28
rrl 1476624 n.2967T>G non_coding_transcript_exon_variant 0.23
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.34
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.22
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.21
inhA 1674892 p.Asn231Asp missense_variant 0.19
inhA 1674903 c.702T>C synonymous_variant 0.15
inhA 1674904 p.Ala235Pro missense_variant 0.15
inhA 1674942 c.741T>G synonymous_variant 0.12
rpsA 1833568 c.27G>C synonymous_variant 0.14
rpsA 1833727 c.186G>C synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.99
rpsA 1834528 c.987T>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103226 c.-184C>G upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.28
PPE35 2170090 p.Pro175Ser missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518747 c.633C>G synonymous_variant 0.12
eis 2714366 p.Val323Leu missense_variant 0.19
eis 2714569 p.Ala255Gly missense_variant 0.21
ahpC 2725954 c.-239C>T upstream_gene_variant 0.4
pepQ 2859680 p.Leu247Val missense_variant 0.26
Rv2752c 3064552 p.Arg547Pro missense_variant 0.19
Rv2752c 3064741 p.Gly484Ala missense_variant 0.3
Rv2752c 3066309 c.-118T>C upstream_gene_variant 0.12
Rv2752c 3066315 c.-124C>T upstream_gene_variant 0.17
Rv2752c 3066330 c.-139G>C upstream_gene_variant 0.12
thyX 3067445 c.501C>G synonymous_variant 0.14
thyX 3067457 c.489C>G synonymous_variant 0.2
thyX 3067465 p.Ile161Val missense_variant 0.2
thyX 3067475 c.471A>G synonymous_variant 0.17
thyX 3067490 c.456C>G synonymous_variant 0.13
thyX 3067493 c.453A>G synonymous_variant 0.12
thyX 3067619 c.327A>C synonymous_variant 0.13
thyX 3067631 c.315C>G synonymous_variant 0.12
thyX 3067652 c.294T>C synonymous_variant 0.13
thyX 3067793 c.153T>C synonymous_variant 0.12
thyX 3067965 c.-20C>G upstream_gene_variant 0.25
ald 3086739 c.-81G>A upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339550 p.Gly145Trp missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642734 c.1200G>C synonymous_variant 0.18
rpoA 3877553 p.Glu319Gln missense_variant 0.15
rpoA 3877571 p.Pro313Ala missense_variant 0.13
rpoA 3877587 c.921A>G synonymous_variant 0.15
rpoA 3877613 p.Ile299Val missense_variant 0.14
rpoA 3877776 c.732T>C synonymous_variant 0.13
rpoA 3877782 c.726T>C synonymous_variant 0.13
rpoA 3877791 c.717C>G synonymous_variant 0.13
rpoA 3878391 c.117T>C synonymous_variant 0.13
clpC1 4038596 c.2109A>G synonymous_variant 0.15
clpC1 4038857 c.1848C>A synonymous_variant 0.25
clpC1 4038860 c.1845G>C synonymous_variant 0.14
clpC1 4038878 c.1827A>G synonymous_variant 0.19
clpC1 4039226 c.1479T>C synonymous_variant 0.12
clpC1 4039274 c.1431G>C synonymous_variant 0.13
clpC1 4039382 c.1323C>A synonymous_variant 0.15
clpC1 4039391 c.1314T>G synonymous_variant 0.14
clpC1 4039397 c.1308A>G synonymous_variant 0.15
clpC1 4039409 c.1296T>C synonymous_variant 0.12
clpC1 4039480 c.1225C>A synonymous_variant 0.12
clpC1 4039481 c.1224T>G synonymous_variant 0.14
clpC1 4039517 c.1188C>G synonymous_variant 0.16
clpC1 4039664 c.1041G>C synonymous_variant 0.15
clpC1 4039694 c.1011G>C synonymous_variant 0.13
clpC1 4039724 c.981A>G synonymous_variant 0.17
clpC1 4039932 p.Gly258Val missense_variant 0.28
clpC1 4039952 c.753T>C synonymous_variant 0.14
embC 4240789 c.927T>C synonymous_variant 0.14
embC 4241056 c.1194C>G synonymous_variant 0.27
embC 4241095 c.1233C>T synonymous_variant 0.13
embC 4242476 p.Pro872Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242742 c.-491C>G upstream_gene_variant 0.12
embA 4242748 c.-485A>G upstream_gene_variant 0.12
embA 4242754 c.-479G>C upstream_gene_variant 0.13
embC 4242764 p.Val968Leu missense_variant 0.13
embC 4242822 p.Val987Gly missense_variant 0.39
embC 4242827 p.Leu989Val missense_variant 0.21
embA 4243460 c.228C>T synonymous_variant 0.99
embA 4244375 c.1143C>G synonymous_variant 0.3
embB 4247041 c.528C>T synonymous_variant 0.27
embB 4248085 c.1572T>C synonymous_variant 0.13
embB 4248097 c.1584C>G synonymous_variant 0.13
embB 4248304 c.1791G>C synonymous_variant 0.13
embB 4248319 c.1806A>G synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.2
ethA 4327672 c.-199G>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.99