TB-Profiler result

Run: ERR6336744
Summary

Run ID: ERR6336744

Sample name:

Date: 02-04-2023 02:01:46

Number of reads: 611767

Percentage reads mapped: 98.87

Strain:

Drug-resistance: HR-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
lineage1.2.1 Indo-Oceanic EAI2 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
katG 2156024 c.87delC frameshift_variant 0.11 isoniazid, isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.15 pyrazinamide
kasA 2519274 p.Gly387Asp missense_variant 0.25 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 5149 c.-91G>A upstream_gene_variant 0.2
gyrB 5175 c.-65T>C upstream_gene_variant 0.25
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6723 p.Arg495Gln missense_variant 0.18
gyrB 6846 p.Asp536Val missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7434 c.134delG frameshift_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7884 p.Arg195Cys missense_variant 0.33
gyrA 8281 p.Val327Ala missense_variant 0.25
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8510 c.1209G>A synonymous_variant 0.22
gyrA 8616 p.Gln439Lys missense_variant 0.18
gyrA 8659 p.Asp453Ala missense_variant 0.17
gyrA 8699 p.Glu466Asp missense_variant 0.13
gyrA 8701 c.1401delC frameshift_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9162 p.Pro621Ser missense_variant 0.2
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9657 p.Thr786Ala missense_variant 0.4
fgd1 490630 c.-153G>A upstream_gene_variant 0.25
fgd1 490921 p.Gln47* stop_gained 0.22
fgd1 491036 p.Val85Ala missense_variant 0.5
fgd1 491709 c.927A>G synonymous_variant 0.1
fgd1 491714 p.His311Arg missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575193 c.-155G>A upstream_gene_variant 0.22
mshA 575202 c.-145delC upstream_gene_variant 0.29
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575416 c.69T>G synonymous_variant 0.11
mshA 575916 p.Asp190Gly missense_variant 0.15
mshA 575980 p.Asp211Glu missense_variant 0.29
mshA 576108 p.Ala254Gly missense_variant 0.67
mshA 576351 p.Asp335Val missense_variant 0.2
mshA 576388 c.1041G>A synonymous_variant 0.29
ccsA 620600 p.Phe237Ser missense_variant 0.5
ccsA 620825 p.Leu312Gln missense_variant 0.25
rpoB 759812 c.6A>G synonymous_variant 0.18
rpoB 760817 p.Glu337Asp missense_variant 0.22
rpoB 761355 p.Val517Met missense_variant 0.25
rpoB 761611 p.Gly602Glu missense_variant 0.17
rpoB 761685 p.Arg627Cys missense_variant 0.2
rpoB 762030 p.Thr742Ser missense_variant 0.29
rpoB 762996 p.Glu1064* stop_gained 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763060 p.Ile1085Ser missense_variant 0.14
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764149 c.780G>A synonymous_variant 0.18
rpoC 765646 p.Gln759His missense_variant 0.29
rpoC 765898 c.2529C>A synonymous_variant 0.12
rpoC 765902 p.Thr845Ala missense_variant 0.13
rpoC 765967 c.2598C>T synonymous_variant 0.13
rpoC 766084 c.2718dupC frameshift_variant 0.13
rpoC 766113 p.Tyr915Ser missense_variant 0.15
rpoC 766119 p.Glu917Ala missense_variant 0.15
rpoC 766321 c.2952C>G synonymous_variant 0.33
rpoC 767189 p.Pro1274Ala missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775806 p.Met892Thr missense_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776386 p.Pro699Ser missense_variant 0.22
mmpL5 776880 p.Asp534Ala missense_variant 0.15
mmpL5 776884 p.Ile533Val missense_variant 0.15
mmpL5 777010 p.Pro491Ser missense_variant 0.13
mmpL5 777337 p.Val382Ile missense_variant 0.18
mmpS5 778486 p.Lys140Asn missense_variant 0.18
mmpL5 778953 c.-473A>T upstream_gene_variant 0.2
mmpL5 779094 c.-614C>T upstream_gene_variant 0.22
mmpL5 779106 c.-626C>T upstream_gene_variant 0.22
mmpS5 779673 c.-768A>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>T upstream_gene_variant 0.17
fbiC 1303063 c.135delC frameshift_variant 0.2
fbiC 1303253 p.Val108Ala missense_variant 0.29
fbiC 1303556 p.Pro209Leu missense_variant 0.22
fbiC 1304010 c.1080G>A synonymous_variant 0.17
fbiC 1304059 c.1129C>T synonymous_variant 0.15
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406365 p.Gly326Arg missense_variant 0.17
embR 1416565 c.783T>C synonymous_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417098 p.Gly84Ser missense_variant 0.18
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471748 n.-98C>G upstream_gene_variant 0.18
rrl 1473500 n.-158C>T upstream_gene_variant 0.22
rrl 1473590 n.-68A>G upstream_gene_variant 0.17
rrl 1473605 n.-53G>A upstream_gene_variant 0.17
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
fabG1 1673367 c.-73G>C upstream_gene_variant 0.25
fabG1 1673553 p.Asp38Glu missense_variant 0.3
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
rpsA 1833358 c.-184C>A upstream_gene_variant 0.17
rpsA 1833622 c.81C>T synonymous_variant 0.15
rpsA 1834525 c.984G>A synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103124 c.-82T>C upstream_gene_variant 0.29
katG 2154227 p.Gly629Arg missense_variant 0.29
katG 2154240 p.Met624Ile missense_variant 0.4
katG 2154343 p.Lys590Arg missense_variant 0.18
katG 2154601 p.Gly504Glu missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155512 c.600G>A synonymous_variant 0.5
katG 2156277 c.-166G>A upstream_gene_variant 0.14
PPE35 2167676 c.2936dupG frameshift_variant 0.25
PPE35 2167714 p.Val967Ile missense_variant 0.2
PPE35 2167768 p.Gly949Ser missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168142 p.Phe824Ser missense_variant 0.12
PPE35 2169691 p.Gly308Ser missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.67
PPE35 2170266 p.Gly116Asp missense_variant 0.33
PPE35 2170271 c.342T>C synonymous_variant 0.29
Rv1979c 2222144 p.Ser341Thr missense_variant 0.5
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222627 p.Gly180Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289003 p.Asp80Val missense_variant 0.15
pncA 2289045 p.Ser66Trp missense_variant 0.15
pncA 2290003 c.-762C>T upstream_gene_variant 0.4
pncA 2290032 c.-791A>G upstream_gene_variant 0.25
pncA 2290034 c.-794_-793delGCinsAT upstream_gene_variant 0.2
pncA 2290106 c.-865C>T upstream_gene_variant 0.22
kasA 2518110 c.-5T>G upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518756 c.642G>C synonymous_variant 0.13
kasA 2518765 c.651G>A synonymous_variant 0.15
kasA 2518809 p.Lys232Arg missense_variant 0.15
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714271 c.1062C>T synonymous_variant 0.33
eis 2714429 p.Pro302Ser missense_variant 0.22
eis 2714949 c.384G>A synonymous_variant 0.15
eis 2715285 p.Met16Ile missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726383 p.Glu64Gly missense_variant 0.4
folC 2746367 p.Ala411Val missense_variant 0.5
folC 2746439 p.Val387Ala missense_variant 0.13
pepQ 2859960 c.459G>A synonymous_variant 0.18
pepQ 2860418 p.Val1Met missense_variant 0.25
pepQ 2860539 c.-121G>A upstream_gene_variant 0.33
Rv2752c 3065086 p.Arg369Thr missense_variant 0.2
Rv2752c 3065217 c.975C>T synonymous_variant 0.12
Rv2752c 3065315 p.Glu293Gln missense_variant 0.14
Rv2752c 3065366 c.826C>T synonymous_variant 0.15
Rv2752c 3065478 c.714C>T synonymous_variant 0.18
Rv2752c 3065549 p.Glu215Lys missense_variant 0.18
Rv2752c 3065582 p.Thr204Ala missense_variant 0.17
Rv2752c 3065786 p.His136Tyr missense_variant 0.15
Rv2752c 3066037 p.His52Arg missense_variant 0.67
Rv2752c 3067053 c.-862C>G upstream_gene_variant 0.14
thyX 3067243 p.Leu235Met missense_variant 0.33
thyX 3067752 p.Ile65Thr missense_variant 0.25
thyX 3068128 c.-183C>T upstream_gene_variant 0.22
thyA 3074459 p.Glu5Lys missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086881 p.Ala21Asp missense_variant 0.22
ald 3087103 p.Leu95Trp missense_variant 0.11
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448515 p.His4Gln missense_variant 0.13
Rv3083 3448516 p.Phe5Val missense_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448720 p.Lys73* stop_gained 0.17
Rv3083 3448787 p.Asp95Val missense_variant 0.18
Rv3083 3449196 c.693C>T synonymous_variant 0.15
Rv3083 3449330 p.Arg276His missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474791 p.Pro262Leu missense_variant 0.15
fprA 3474914 p.Ala303Val missense_variant 0.22
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
whiB7 3568571 p.Glu37Lys missense_variant 0.4
whiB7 3568580 p.Ala34Thr missense_variant 0.4
whiB7 3568797 c.-118G>A upstream_gene_variant 0.18
Rv3236c 3612193 c.924C>T synonymous_variant 0.18
Rv3236c 3612327 c.789delG frameshift_variant 0.14
Rv3236c 3612403 c.714G>A synonymous_variant 0.15
Rv3236c 3612536 p.Gly194Glu missense_variant 0.15
Rv3236c 3612895 c.222T>A synonymous_variant 0.12
fbiA 3640478 c.-65G>A upstream_gene_variant 0.17
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640654 p.Asp38Asn missense_variant 0.29
fbiA 3640660 p.Gln40* stop_gained 0.25
fbiB 3640881 c.-654G>A upstream_gene_variant 0.17
fbiA 3641387 p.Thr282Ile missense_variant 0.33
fbiB 3641627 c.93C>T synonymous_variant 0.29
fbiB 3641955 p.Gly141Ser missense_variant 0.2
fbiB 3642269 c.735C>T synonymous_variant 0.2
alr 3840310 c.1111C>A synonymous_variant 0.2
alr 3840842 c.579G>C synonymous_variant 0.29
rpoA 3878334 c.174T>A synonymous_variant 0.33
ddn 3986935 p.Arg31His missense_variant 0.13
clpC1 4039942 c.763C>T synonymous_variant 0.17
clpC1 4040057 c.648C>T synonymous_variant 0.18
clpC1 4040517 p.Val63Thr missense_variant 1.0
clpC1 4040536 p.Glu57Lys missense_variant 0.18
clpC1 4040548 p.Gly53Arg missense_variant 0.15
panD 4043903 p.Asn127His missense_variant 0.15
panD 4044172 p.Asp37Gly missense_variant 0.15
embC 4239822 c.-41C>A upstream_gene_variant 0.17
embC 4240295 p.Ser145Gly missense_variant 0.15
embC 4240329 p.Thr156Ile missense_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241080 p.Ile406Met missense_variant 0.33
embC 4241087 p.Thr409Ala missense_variant 0.33
embC 4241360 p.Asn500Asp missense_variant 0.67
embC 4241489 p.Ala543Thr missense_variant 0.13
embC 4241595 p.Ala578Val missense_variant 0.14
embC 4241988 p.Ala709Val missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242837 p.Pro992Leu missense_variant 0.17
embA 4243427 c.195G>A synonymous_variant 0.13
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243898 c.666C>T synonymous_variant 0.25
embA 4244009 c.777G>A synonymous_variant 0.12
embA 4244030 c.798C>T synonymous_variant 0.2
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244884 p.Arg551Gln missense_variant 0.12
embA 4245028 p.Ser599Asn missense_variant 0.13
embA 4245471 p.Ala747Thr missense_variant 0.33
embA 4245654 p.Asp808Asn missense_variant 0.29
embB 4245806 c.-708G>A upstream_gene_variant 0.22
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246311 p.Gly1027Ser missense_variant 0.29
embB 4246584 p.Arg24Pro missense_variant 0.25
embB 4247087 c.574C>T synonymous_variant 0.29
embB 4247426 p.Gly305Thr missense_variant 0.18
embB 4247437 c.924A>G synonymous_variant 0.2
embB 4247440 c.927C>G synonymous_variant 0.2
embB 4247441 p.Ala310Ser missense_variant 0.2
embB 4247446 p.Asp311Glu missense_variant 0.2
embB 4247449 c.936C>T synonymous_variant 0.2
embB 4247452 c.939C>G synonymous_variant 0.2
embB 4247458 c.945C>T synonymous_variant 0.2
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247778 p.Ser422Phe missense_variant 0.22
embB 4247905 c.1392G>A synonymous_variant 0.5
embB 4247918 p.Arg469Gly missense_variant 0.5
embB 4248324 p.Ala604Gly missense_variant 0.25
embB 4248995 p.Gly828Ser missense_variant 0.17
embB 4249755 p.Gly1081Ala missense_variant 0.14
embB 4249761 p.Ala1083Gly missense_variant 0.17
aftB 4267114 p.Leu575Phe missense_variant 0.15
aftB 4267486 c.1351C>T synonymous_variant 0.33
aftB 4267491 p.Ala449Val missense_variant 0.33
aftB 4267496 p.Glu447Asp missense_variant 0.33
aftB 4267522 p.Leu439Phe missense_variant 0.33
aftB 4267638 p.Thr400Ile missense_variant 0.13
aftB 4267995 p.Met281Thr missense_variant 0.2
aftB 4268601 p.Leu79Arg missense_variant 0.17
aftB 4268607 c.229_230insG frameshift_variant 0.12
aftB 4268683 p.Gly52Arg missense_variant 0.11
aftB 4268861 c.-25T>G upstream_gene_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269635 p.Ser67Pro missense_variant 0.29
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4269997 c.-164C>T upstream_gene_variant 0.33
ethA 4327629 c.-156C>T upstream_gene_variant 0.22
ethR 4327748 p.Ser67Phe missense_variant 0.33
whiB6 4338330 c.192C>T synonymous_variant 1.0
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
whiB6 4338664 c.-143C>T upstream_gene_variant 0.18
whiB6 4338687 c.-166G>A upstream_gene_variant 0.15
whiB6 4338703 c.-182T>C upstream_gene_variant 0.18
whiB6 4338707 c.-186A>C upstream_gene_variant 0.18
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407899 c.304C>A synonymous_variant 0.4
gid 4407997 p.Gly69Val missense_variant 1.0
gid 4408194 c.9G>A synonymous_variant 0.29