TB-Profiler result

Run: ERR6336765
Summary

Run ID: ERR6336765

Sample name:

Date: 02-04-2023 02:02:32

Number of reads: 1066646

Percentage reads mapped: 98.12

Strain:

Drug-resistance: HR-TB

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 1.0
lineage1.2.1.2.1 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
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5511 p.Ser91Phe missense_variant 0.25
gyrB 5520 p.Pro94Arg missense_variant 0.22
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 8414 c.1113C>T synonymous_variant 0.2
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8535 p.Glu412Lys missense_variant 0.15
gyrA 8843 c.1542G>A synonymous_variant 0.17
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9144 p.Arg615Cys missense_variant 0.17
gyrA 9158 c.1857C>T synonymous_variant 0.17
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9358 p.Thr686Ile missense_variant 0.29
gyrA 9562 p.Met754Thr missense_variant 0.12
gyrA 9569 p.Asp756Glu missense_variant 0.18
fgd1 490885 p.Ala35Thr missense_variant 0.14
fgd1 490993 p.Gly71Ser missense_variant 0.29
fgd1 491129 p.Thr116Asn missense_variant 0.25
fgd1 491131 p.Gly117Arg missense_variant 0.2
fgd1 491227 p.Asp149Asn missense_variant 0.15
fgd1 491262 c.480C>T synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576239 p.Ala298Pro missense_variant 0.33
ccsA 619791 c.-100G>A upstream_gene_variant 0.18
ccsA 620014 p.Arg42Cys missense_variant 0.4
ccsA 620085 c.195G>A synonymous_variant 0.4
ccsA 620371 p.Ala161Ser missense_variant 0.18
rpoB 759979 p.Leu58Pro missense_variant 0.11
rpoB 760008 p.Ala68Thr missense_variant 0.18
rpoB 760572 p.Leu256Met missense_variant 0.15
rpoB 760604 c.798G>A synonymous_variant 0.14
rpoB 760605 p.Ala267Thr missense_variant 0.14
rpoB 761133 c.1327T>C synonymous_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.57
rpoB 761162 c.1356G>T synonymous_variant 0.4
rpoB 761710 p.Val635Asp missense_variant 0.6
rpoB 761713 p.Val636Asp missense_variant 0.6
rpoB 761828 c.2022C>T synonymous_variant 0.13
rpoB 762307 p.Pro834Gln missense_variant 0.5
rpoB 762631 p.Ala942Val missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763595 p.Glu76Lys missense_variant 0.18
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764560 c.1191T>C synonymous_variant 0.33
rpoC 765608 p.Asp747Asn missense_variant 0.12
rpoC 765941 p.Lys858Glu missense_variant 0.13
rpoC 765966 p.Arg866His missense_variant 0.29
rpoC 766073 c.2706delC frameshift_variant 0.14
rpoC 766163 p.Glu932Lys missense_variant 0.25
rpoC 766171 c.2802C>T synonymous_variant 0.2
rpoC 766199 c.2830C>T synonymous_variant 0.15
rpoC 766782 p.Val1138Ala missense_variant 0.15
rpoC 766912 c.3543C>T synonymous_variant 0.18
rpoC 766919 p.Ala1184Thr missense_variant 0.22
rpoC 767205 p.Arg1279His missense_variant 0.13
rpoC 767271 p.Thr1301Ser missense_variant 0.18
rpoC 767320 c.3951G>A splice_region_variant&stop_retained_variant 0.15
mmpL5 775633 p.Gln950* stop_gained 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775925 c.2556G>T synonymous_variant 0.12
mmpL5 775931 c.2550C>T synonymous_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777410 c.1071A>T synonymous_variant 0.25
mmpL5 777418 p.Pro355Thr missense_variant 0.22
mmpL5 777479 c.1002C>T synonymous_variant 0.15
mmpL5 777722 c.759C>T synonymous_variant 0.25
rpsL 781361 c.-199G>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800991 c.183G>A synonymous_variant 0.17
fbiC 1302879 c.-52T>C upstream_gene_variant 0.13
fbiC 1303591 p.Arg221Gly missense_variant 0.2
fbiC 1303678 p.Arg250Trp missense_variant 0.15
fbiC 1304016 c.1086C>T synonymous_variant 0.15
fbiC 1304197 p.Gly423Ser missense_variant 0.67
fbiC 1304791 p.Val621Ile missense_variant 0.25
fbiC 1305280 p.Ile784Phe missense_variant 0.13
Rv1258c 1406200 p.Leu381Phe missense_variant 0.15
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406471 c.870C>A synonymous_variant 0.17
Rv1258c 1406704 p.Ala213Thr missense_variant 0.17
embR 1416490 c.858G>A synonymous_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.13
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
fabG1 1674010 p.Thr191Ser missense_variant 0.12
fabG1 1674059 p.Pro207Leu missense_variant 0.18
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674687 c.486G>A synonymous_variant 0.2
rpsA 1834040 p.Lys167Glu missense_variant 0.29
rpsA 1834562 p.Gly341Ser missense_variant 0.22
tlyA 1917825 c.-115G>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918102 p.Val55Met missense_variant 0.25
tlyA 1918426 p.Val163Met missense_variant 0.13
tlyA 1918710 c.771G>A synonymous_variant 0.17
ndh 2102079 p.Asp322Asn missense_variant 0.17
ndh 2102127 p.Leu306Met missense_variant 0.2
ndh 2102308 c.735G>C synonymous_variant 0.18
ndh 2102397 p.Ala216Ser missense_variant 0.29
ndh 2103167 c.-125A>G upstream_gene_variant 0.18
ndh 2103220 c.-178C>G upstream_gene_variant 0.25
ndh 2103227 c.-185T>C upstream_gene_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155310 p.Gly268Ser missense_variant 0.33
katG 2155416 c.696G>A synonymous_variant 0.18
katG 2155638 p.Lys158Asn missense_variant 0.18
katG 2155656 c.456G>A synonymous_variant 0.22
katG 2156346 c.-235T>G upstream_gene_variant 0.15
katG 2156493 c.-382C>T upstream_gene_variant 0.14
katG 2156517 c.-406C>T upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167982 c.2631C>G synonymous_variant 0.13
PPE35 2169961 p.Gly218Ser missense_variant 0.14
PPE35 2169986 c.627G>A synonymous_variant 0.33
PPE35 2170048 p.Leu189Val missense_variant 0.75
PPE35 2170053 p.Thr187Ser missense_variant 0.75
PPE35 2170300 p.Val105Ile missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288699 c.543G>A synonymous_variant 0.33
pncA 2288799 p.Arg148His missense_variant 0.15
pncA 2289350 c.-109G>T upstream_gene_variant 0.12
pncA 2289529 c.-288G>T upstream_gene_variant 0.13
pncA 2289815 c.-574C>T upstream_gene_variant 0.33
pncA 2289884 c.-643G>A upstream_gene_variant 0.4
pncA 2290109 c.-868C>T upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518390 c.276A>G synonymous_variant 0.13
kasA 2518392 p.Gln93Arg missense_variant 0.13
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519321 p.Gly403Arg missense_variant 0.2
eis 2714408 p.Gly309Ser missense_variant 0.2
eis 2714970 c.363C>T synonymous_variant 0.29
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726694 p.Leu168Phe missense_variant 0.18
folC 2746625 p.Ala325Val missense_variant 0.22
folC 2747118 p.Ala161Pro missense_variant 0.67
folC 2747135 p.Leu155His missense_variant 0.67
pepQ 2859399 p.Asp340Glu missense_variant 0.11
pepQ 2859592 p.Ala276Val missense_variant 0.22
pepQ 2860048 p.Ala124Val missense_variant 0.17
ribD 2986711 c.-128G>T upstream_gene_variant 0.2
ribD 2986790 c.-49G>A upstream_gene_variant 0.14
ribD 2987528 c.693delC frameshift_variant 0.17
Rv2752c 3064922 p.Glu424Lys missense_variant 0.12
Rv2752c 3065336 p.Leu286Phe missense_variant 0.14
Rv2752c 3065492 p.Ile234Val missense_variant 0.12
Rv2752c 3065533 p.Pro220Leu missense_variant 0.2
Rv2752c 3066135 c.57C>T synonymous_variant 0.18
Rv2752c 3066171 c.20delC frameshift_variant 0.14
Rv2752c 3066240 c.-49G>A upstream_gene_variant 0.14
Rv2752c 3067134 c.-943C>T upstream_gene_variant 0.2
thyA 3074038 p.Pro145Leu missense_variant 0.17
thyA 3074044 p.Leu143Arg missense_variant 0.17
thyA 3074471 p.Val1Met missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087725 c.907delG frameshift_variant 0.22
fbiD 3339090 c.-28C>T upstream_gene_variant 0.4
fbiD 3339238 p.Ala41Pro missense_variant 0.25
fbiD 3339284 c.170_171delGC frameshift_variant 0.25
fbiD 3339290 p.Ser58Leu missense_variant 0.33
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448358 c.-146G>T upstream_gene_variant 0.29
Rv3083 3448361 c.-143G>T upstream_gene_variant 0.22
Rv3083 3448588 c.87_88delCA frameshift_variant 0.15
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448858 p.Ala119Thr missense_variant 0.15
Rv3083 3449937 p.Ile478Met missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474033 c.27G>A synonymous_variant 0.5
fprA 3474355 c.350delA frameshift_variant 0.18
fprA 3474363 c.357G>A synonymous_variant 0.15
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474600 c.594G>A synonymous_variant 0.17
fprA 3475090 p.Arg362Cys missense_variant 0.13
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475344 p.Ser446Arg missense_variant 0.22
fprA 3475351 p.Glu449Lys missense_variant 0.22
fprA 3475356 c.1350G>A synonymous_variant 0.22
whiB7 3568488 c.191delG frameshift_variant 1.0
whiB7 3568561 p.Lys40Arg missense_variant 0.12
Rv3236c 3613161 c.-45A>T upstream_gene_variant 0.12
Rv3236c 3613297 c.-181C>T upstream_gene_variant 0.18
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640616 p.Leu25Pro missense_variant 0.17
fbiB 3640879 c.-656C>T upstream_gene_variant 0.13
fbiB 3642543 p.Arg337Cys missense_variant 0.15
rpoA 3877626 c.882C>T synonymous_variant 0.17
rpoA 3877881 c.627G>A synonymous_variant 0.17
rpoA 3877885 p.Leu208Arg missense_variant 0.13
rpoA 3877891 p.Asp206Val missense_variant 0.13
rpoA 3877897 p.Pro204Gln missense_variant 0.14
rpoA 3878086 p.Glu141Gly missense_variant 0.12
rpoA 3878567 c.-60C>G upstream_gene_variant 0.23
clpC1 4038899 c.1806C>G synonymous_variant 0.25
clpC1 4039251 p.Ala485Val missense_variant 0.17
clpC1 4040002 p.His235Asn missense_variant 0.17
clpC1 4040051 c.654C>T synonymous_variant 0.29
clpC1 4040057 c.648C>T synonymous_variant 0.29
clpC1 4040170 p.Thr179Ala missense_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239694 c.-168delA upstream_gene_variant 0.2
embC 4239725 c.-138G>A upstream_gene_variant 0.18
embC 4240360 c.498C>T synonymous_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241212 c.1350G>A synonymous_variant 0.22
embC 4241231 p.Arg457Gly missense_variant 0.18
embC 4241281 c.1419G>A synonymous_variant 0.2
embC 4241470 c.1608C>T synonymous_variant 0.13
embC 4242530 p.Arg890* stop_gained 0.5
embC 4243121 p.Ser1087Cys missense_variant 0.18
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243608 c.377delC frameshift_variant 0.5
embA 4243704 p.Gly158Ser missense_variant 0.33
embA 4243723 p.Pro164Leu missense_variant 0.29
embA 4244011 p.Thr260Ile missense_variant 0.4
embA 4244417 c.1185G>A synonymous_variant 0.5
embA 4244420 c.1188G>C synonymous_variant 1.0
embB 4245950 c.-564G>A upstream_gene_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246105 p.Pro958Leu missense_variant 0.17
embB 4246430 c.-84C>G upstream_gene_variant 0.22
embB 4246475 c.-39G>A upstream_gene_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.42
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246563 p.Leu17Trp missense_variant 0.36
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4246584 p.Arg24Pro missense_variant 0.4
embB 4246814 p.Thr101Ala missense_variant 0.22
embB 4246886 p.Val125Ile missense_variant 0.18
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248670 c.2157C>T synonymous_variant 0.14
embB 4248766 c.2253C>T synonymous_variant 0.13
embB 4248967 c.2454G>C synonymous_variant 0.13
embB 4249395 p.Ile961Thr missense_variant 0.18
embB 4249434 p.Leu974Pro missense_variant 0.13
embB 4249494 p.Phe994Ser missense_variant 0.12
aftB 4267906 p.Val311Met missense_variant 0.4
aftB 4267910 c.927G>A synonymous_variant 0.4
aftB 4268925 c.-89G>A upstream_gene_variant 0.18
ubiA 4268944 c.889dupG frameshift_variant 0.18
ubiA 4269115 p.Arg240Pro missense_variant 0.4
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269498 p.Thr112Met missense_variant 0.14
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4269908 c.-75C>T upstream_gene_variant 0.22
ubiA 4269941 c.-108C>T upstream_gene_variant 0.17
ethA 4326921 p.Ala185Pro missense_variant 0.2
ethR 4326934 c.-615C>T upstream_gene_variant 0.17
ethA 4327641 c.-168G>A upstream_gene_variant 0.2
ethA 4328187 c.-714G>A upstream_gene_variant 0.22
whiB6 4338361 p.Arg54Gln missense_variant 1.0
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 4407805 p.Ala133Val missense_variant 0.25
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408063 p.Arg47Pro missense_variant 0.14
gid 4408351 c.-149G>A upstream_gene_variant 0.4