TB-Profiler result

Run: ERR6336766
Summary

Run ID: ERR6336766

Sample name:

Date: 02-04-2023 02:02:34

Number of reads: 954853

Percentage reads mapped: 98.93

Strain: lineage1.2.1.2.1

Drug-resistance: Other

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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 Indo-Oceanic NA 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
tlyA 1918487 p.Pro183Leu missense_variant 0.15 capreomycin
pncA 2289036 p.Pro69Leu missense_variant 0.13 pyrazinamide
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 5234 c.-6C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7376 c.75G>A synonymous_variant 0.13
gyrA 7418 c.117C>T synonymous_variant 0.29
gyrA 7423 p.Leu41Gln missense_variant 0.33
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7720 p.Glu140Gly missense_variant 0.12
gyrA 7728 p.Arg143Gly missense_variant 0.12
gyrA 7781 c.480G>C synonymous_variant 0.22
gyrA 7795 p.Val165Ala missense_variant 0.22
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8833 p.Ile511Thr missense_variant 0.11
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490864 p.Glu28Lys missense_variant 0.2
fgd1 491082 c.300T>G synonymous_variant 0.11
fgd1 491309 p.Ala176Gly missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576099 p.Asp251Gly missense_variant 0.67
ccsA 619929 c.39C>T synonymous_variant 0.12
ccsA 620853 c.963G>C synonymous_variant 0.14
rpoB 760937 c.1131G>A synonymous_variant 0.17
rpoB 761164 p.Gly453Glu missense_variant 0.33
rpoB 761502 p.Pro566Ser missense_variant 0.22
rpoB 761701 p.Ala632Val missense_variant 0.29
rpoB 761710 p.Val635Asp missense_variant 0.38
rpoB 761713 p.Val636Asp missense_variant 0.44
rpoB 762140 c.2334G>C synonymous_variant 0.25
rpoB 762285 p.Arg827Cys missense_variant 0.22
rpoC 762701 c.-669T>C upstream_gene_variant 0.12
rpoB 762954 p.Pro1050Ser missense_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 763901 p.Glu178Lys missense_variant 0.25
rpoC 763981 c.612G>A synonymous_variant 0.67
rpoC 764383 c.1014C>T synonymous_variant 0.2
rpoC 764514 p.Phe382Ser missense_variant 0.12
rpoC 764686 c.1317C>T synonymous_variant 0.25
rpoC 764809 c.1440C>T synonymous_variant 0.14
rpoC 765016 c.1647C>G synonymous_variant 0.13
rpoC 766258 c.2889T>A synonymous_variant 0.18
rpoC 766444 c.3075C>T synonymous_variant 0.2
rpoC 766468 p.Glu1033Asp missense_variant 0.22
rpoC 766533 p.Leu1055His missense_variant 0.25
rpoC 766604 p.Lys1079Glu missense_variant 0.14
rpoC 766614 c.3247_3248delCG frameshift_variant 0.14
rpoC 766692 p.Gly1108Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776233 p.Pro750Ala missense_variant 0.13
mmpL5 776272 p.Lys737Glu missense_variant 0.2
mmpL5 777170 p.His437Arg missense_variant 0.15
mmpL5 777514 p.Cys323Arg missense_variant 0.11
mmpL5 777554 p.Val309Gly missense_variant 0.17
mmpL5 778161 p.Ala107Gly missense_variant 0.14
mmpR5 778415 c.-575C>T upstream_gene_variant 0.14
mmpL5 778452 p.Thr10Arg missense_variant 0.2
mmpS5 778491 p.Val139Met missense_variant 0.13
mmpL5 779271 c.-791C>T upstream_gene_variant 0.22
mmpR5 779276 p.Arg96Gln missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781688 c.129G>A synonymous_variant 0.13
fbiC 1303450 p.Val174Met missense_variant 0.5
fbiC 1303564 p.Gly212Ser missense_variant 0.13
fbiC 1304288 p.Ile453Asn missense_variant 0.17
fbiC 1304639 p.Arg570Gln missense_variant 0.13
fbiC 1304668 p.Ser580Pro missense_variant 0.25
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406755 p.Ala196Thr missense_variant 0.67
Rv1258c 1407191 c.150G>A synonymous_variant 0.17
embR 1416631 c.717C>T synonymous_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.21
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.19
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
inhA 1673913 c.-289C>G upstream_gene_variant 0.15
fabG1 1674013 c.575delG frameshift_variant 0.18
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674660 c.459G>A synonymous_variant 0.14
rpsA 1833864 p.Gln108Arg missense_variant 0.13
rpsA 1834871 p.Gly444Ser missense_variant 0.67
tlyA 1917857 c.-83C>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918121 p.Ala61Val missense_variant 0.2
ndh 2101665 p.Lys460Glu missense_variant 0.22
ndh 2102397 p.Ala216Thr missense_variant 0.22
ndh 2102469 c.574C>T synonymous_variant 0.14
ndh 2102499 p.Gly182Ser missense_variant 0.14
ndh 2103175 c.-133G>A upstream_gene_variant 0.18
katG 2154431 p.His561Tyr missense_variant 0.18
katG 2154449 p.Ala555Thr missense_variant 0.15
katG 2154612 c.1500G>A synonymous_variant 0.18
katG 2154620 p.Arg498Gly missense_variant 0.22
katG 2154627 c.1485T>G synonymous_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156342 c.-231G>A upstream_gene_variant 0.25
katG 2156348 c.-237A>G upstream_gene_variant 0.25
katG 2156521 c.-410C>T upstream_gene_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170430 c.183A>G synonymous_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517965 c.-150C>G upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519051 p.Thr313Pro missense_variant 0.67
kasA 2519273 p.Gly387Ser missense_variant 0.18
eis 2714634 c.699C>T synonymous_variant 0.17
eis 2714735 c.598C>T synonymous_variant 0.29
eis 2715051 c.282C>G synonymous_variant 0.29
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746543 c.1056C>G synonymous_variant 0.29
folC 2747097 p.Val168Ile missense_variant 0.4
folC 2747132 p.Thr156Ile missense_variant 0.33
folC 2747319 p.Gly94Ser missense_variant 0.2
folC 2747651 c.-53C>T upstream_gene_variant 0.5
pepQ 2859620 p.Gly267Ser missense_variant 0.33
ribD 2986797 c.-42C>T upstream_gene_variant 0.15
ribD 2987095 p.Gly86Val missense_variant 0.14
ribD 2987415 p.Glu193Lys missense_variant 0.15
Rv2752c 3064828 p.Gly455Asp missense_variant 0.4
Rv2752c 3064841 p.Gly451Ser missense_variant 0.22
Rv2752c 3065007 c.1185G>A synonymous_variant 0.5
Rv2752c 3065382 p.Met270Ile missense_variant 0.13
Rv2752c 3065515 p.Ile226Ser missense_variant 0.29
Rv2752c 3065538 c.654G>A synonymous_variant 0.33
Rv2752c 3065545 p.Ser216Asn missense_variant 0.25
Rv2752c 3065646 c.546C>T synonymous_variant 0.2
thyX 3067798 p.Pro50Ser missense_variant 0.13
thyA 3074117 c.355C>T synonymous_variant 0.14
thyA 3074454 c.18C>T synonymous_variant 0.14
thyA 3074492 c.-21T>C upstream_gene_variant 0.29
thyA 3074493 c.-22C>A upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087749 c.930C>T synonymous_variant 0.14
fbiD 3339099 c.-19A>G upstream_gene_variant 0.12
fbiD 3339135 c.18C>T synonymous_variant 0.12
fbiD 3339246 c.129C>T synonymous_variant 0.33
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448565 p.Cys21Tyr missense_variant 0.25
Rv3083 3448573 p.Thr24Ser missense_variant 0.33
Rv3083 3448627 p.Gly42Ser missense_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448747 c.244C>A synonymous_variant 0.2
Rv3083 3448825 p.Glu108Lys missense_variant 0.17
Rv3083 3449230 p.Gly243Ser missense_variant 0.2
fprA 3473888 c.-119G>A upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474225 c.219C>T synonymous_variant 0.12
fprA 3474252 c.246G>A synonymous_variant 0.15
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612113 c.1003delG frameshift_variant 0.18
Rv3236c 3612169 c.947delA frameshift_variant 0.33
Rv3236c 3612533 p.Ala195Val missense_variant 0.14
Rv3236c 3612664 c.453G>A synonymous_variant 0.5
Rv3236c 3613221 c.-105C>T upstream_gene_variant 0.2
Rv3236c 3613291 c.-175G>A upstream_gene_variant 0.2
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3641048 p.Phe169Tyr missense_variant 0.15
fbiB 3641760 p.Lys76Glu missense_variant 0.12
alr 3840284 p.Trp379* stop_gained 0.12
alr 3840338 c.1083C>T synonymous_variant 0.13
alr 3840380 p.Met347Ile missense_variant 0.17
alr 3840547 p.Gly292Ser missense_variant 0.24
alr 3840619 p.Asp268Asn missense_variant 0.2
alr 3840683 c.738G>A synonymous_variant 0.17
alr 3841229 c.192G>T synonymous_variant 0.22
rpoA 3877558 p.Pro317His missense_variant 0.4
rpoA 3877612 p.Ile299Asn missense_variant 0.13
rpoA 3878199 c.309T>C synonymous_variant 0.11
rpoA 3878567 c.-60C>G upstream_gene_variant 0.25
rpoA 3878630 c.-123G>C upstream_gene_variant 0.33
rpoA 3878639 c.-132C>G upstream_gene_variant 0.29
rpoA 3878641 c.-135delG upstream_gene_variant 0.29
rpoA 3878707 c.-200C>G upstream_gene_variant 0.12
clpC1 4038198 p.Gly836Glu missense_variant 0.25
clpC1 4038943 p.Arg588Trp missense_variant 0.13
clpC1 4039009 c.1696C>T synonymous_variant 0.14
clpC1 4039034 c.1671C>T synonymous_variant 0.17
clpC1 4039805 c.900C>T synonymous_variant 0.22
clpC1 4039916 c.789T>C synonymous_variant 0.11
clpC1 4040095 p.Leu204Phe missense_variant 0.17
clpC1 4040331 p.Val125Ala missense_variant 0.13
clpC1 4040345 c.360C>T synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044437 c.-156C>T upstream_gene_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240962 p.Leu367Pro missense_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241427 p.Leu522Pro missense_variant 0.2
embC 4241665 c.1803G>A synonymous_variant 0.5
embC 4242260 p.Met800Val missense_variant 0.22
embA 4242427 c.-806A>G upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242962 p.Gly1034Ser missense_variant 0.15
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243715 c.483C>G synonymous_variant 0.2
embA 4244040 p.Thr270Ala missense_variant 0.17
embA 4244048 c.816C>T synonymous_variant 0.15
embA 4244076 c.847delG frameshift_variant 0.11
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244913 c.1681C>T synonymous_variant 0.18
embB 4245719 c.-795G>A upstream_gene_variant 0.25
embA 4245858 p.Ala876Thr missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246925 p.Glu138Gln missense_variant 0.14
embB 4246944 p.Gln144Pro missense_variant 0.2
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247755 c.1242C>T synonymous_variant 0.25
embB 4247999 p.Asp496Asn missense_variant 0.14
embB 4248575 p.Phe688Leu missense_variant 0.33
embB 4248850 c.2337G>T synonymous_variant 0.22
embB 4249116 p.Pro868Arg missense_variant 0.13
embB 4249596 p.Trp1028* stop_gained 0.22
aftB 4267462 p.Gln459* stop_gained 0.17
aftB 4267506 p.Asn444Ile missense_variant 0.13
aftB 4267512 p.Leu442Arg missense_variant 0.13
aftB 4267528 p.Ala437Thr missense_variant 0.15
aftB 4267554 p.Asp428Gly missense_variant 0.15
aftB 4267637 c.1200C>T synonymous_variant 0.17
aftB 4267862 p.Tyr325* stop_gained 0.12
aftB 4268622 p.Trp72* stop_gained 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4270026 c.-193C>A upstream_gene_variant 0.33
ethA 4327908 c.-435T>C upstream_gene_variant 0.15
whiB6 4338276 c.246C>T synonymous_variant 0.25
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 4407720 c.483C>T synonymous_variant 0.13
gid 4407796 p.Ser136Leu missense_variant 0.13
gid 4407852 c.351G>A synonymous_variant 0.12
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407964 p.Ala80Val missense_variant 0.2
gid 4408036 p.Gly56Asp missense_variant 0.13
gid 4408079 p.Gly42Ser missense_variant 0.14