TB-Profiler result

Run: ERR6336761
Summary

Run ID: ERR6336761

Sample name:

Date: 02-04-2023 02:02:22

Number of reads: 721471

Percentage reads mapped: 99.09

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 0.99
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
embB 4247583 p.Ala357Val missense_variant 0.25 ethambutol
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 6112 p.Met291Ile missense_variant 1.0
gyrB 7158 c.1931_1933dupCCG disruptive_inframe_insertion 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7575 p.Ile92Val missense_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8745 p.Glu482Lys missense_variant 0.25
gyrA 9055 p.Pro585Leu missense_variant 0.12
gyrA 9063 c.1765delC frameshift_variant 0.2
gyrA 9076 p.Arg592Pro missense_variant 0.2
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
gyrA 9336 p.Gln679* stop_gained 0.14
fgd1 490852 p.Ala24Thr missense_variant 0.18
fgd1 491109 c.327G>A synonymous_variant 0.33
fgd1 491172 c.390C>T synonymous_variant 0.4
fgd1 491247 c.465C>T synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.4
mshA 576450 p.Pro368Arg missense_variant 0.25
mshA 576766 c.1419G>C synonymous_variant 0.22
mshA 576772 c.1425T>A synonymous_variant 0.22
ccsA 620072 p.Pro61Leu missense_variant 0.29
ccsA 620348 p.Gly153Glu missense_variant 0.22
rpoB 759893 c.87G>A synonymous_variant 0.12
rpoB 760707 p.Asp301Asn missense_variant 0.12
rpoB 761073 p.Glu423Lys missense_variant 0.13
rpoB 761152 p.Leu449Gln missense_variant 0.33
rpoB 761280 p.Gly492Ser missense_variant 0.2
rpoB 761848 p.Cys681Tyr missense_variant 0.5
rpoB 762813 p.Met1003Leu missense_variant 0.33
rpoC 762848 c.-522G>A upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763594 c.225C>T synonymous_variant 0.2
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764068 c.699G>A synonymous_variant 0.12
rpoC 764526 p.Arg386His missense_variant 0.14
rpoC 765374 p.Gly669Ser missense_variant 0.13
rpoC 765683 p.Glu772Lys missense_variant 0.14
rpoC 766074 p.Ala902Val missense_variant 0.2
rpoC 766292 p.Cys975Arg missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777671 c.810G>A synonymous_variant 0.18
mmpR5 778037 c.-953G>A upstream_gene_variant 0.17
mmpL5 778131 p.Gln117Arg missense_variant 0.12
mmpR5 778223 c.-767G>A upstream_gene_variant 0.12
mmpS5 778574 p.Ser111Phe missense_variant 0.13
mmpL5 779178 c.-698G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801160 p.Ser118Pro missense_variant 0.12
fbiC 1302763 c.-168G>A upstream_gene_variant 0.13
fbiC 1302995 p.Asn22Ile missense_variant 0.12
fbiC 1303490 p.Leu187Pro missense_variant 0.33
fbiC 1304183 p.Ala418Glu missense_variant 0.2
fbiC 1304675 p.Gly582Glu missense_variant 0.15
fbiC 1304679 c.1749G>A synonymous_variant 0.15
fbiC 1304892 c.1962C>T synonymous_variant 0.2
fbiC 1304931 c.2001C>T synonymous_variant 0.13
fbiC 1305248 p.Ala773Val missense_variant 0.13
Rv1258c 1406117 c.1224A>G synonymous_variant 0.29
Rv1258c 1406227 p.Asp372Asn missense_variant 0.33
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406539 p.Ala268Thr missense_variant 0.17
embR 1416751 p.Phe199Leu missense_variant 0.12
embR 1416905 p.Pro148Leu missense_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
atpE 1461169 p.Gln42Arg missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674388 p.Leu63Phe missense_variant 0.29
inhA 1674816 c.615T>C synonymous_variant 0.33
rpsA 1834388 p.Pro283Ser missense_variant 0.17
rpsA 1834392 p.Trp284Leu missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918399 p.Asp154His missense_variant 0.22
tlyA 1918415 p.Ser159Leu missense_variant 0.29
ndh 2103227 c.-185T>C upstream_gene_variant 0.25
katG 2153901 p.Phe737Leu missense_variant 0.17
katG 2154012 c.2100C>T synonymous_variant 0.18
katG 2154281 p.Leu611Phe missense_variant 0.13
katG 2154284 c.1828C>T synonymous_variant 0.13
katG 2154346 p.Pro589Leu missense_variant 0.12
katG 2154538 p.Gln525Arg missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154822 c.1290G>A synonymous_variant 0.12
katG 2155884 c.228G>A synonymous_variant 0.25
katG 2155914 c.198G>A synonymous_variant 0.18
katG 2156337 c.-226G>A upstream_gene_variant 0.29
katG 2156386 c.-275G>A upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.18
PPE35 2170210 p.Ala135Thr missense_variant 0.14
Rv1979c 2222051 c.1114C>T synonymous_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222366 p.Tyr267His missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288857 p.Asp129Asn missense_variant 0.12
pncA 2289008 c.234C>T synonymous_variant 0.13
pncA 2289272 c.-31C>T upstream_gene_variant 0.33
pncA 2289534 c.-293G>A upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518323 p.Ser70Asn missense_variant 0.12
kasA 2518531 c.417G>A synonymous_variant 0.12
kasA 2518841 p.Gly243Ser missense_variant 0.4
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519306 p.Val398Ile missense_variant 0.22
eis 2714197 p.Asp379Gly missense_variant 0.12
eis 2714209 p.Leu375Ser missense_variant 0.14
eis 2714949 c.384G>A synonymous_variant 1.0
ahpC 2726027 c.-166C>T upstream_gene_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746324 c.1275C>T synonymous_variant 0.5
pepQ 2859415 p.Gly335Asp missense_variant 0.15
pepQ 2859794 p.Asp209Asn missense_variant 0.14
pepQ 2859857 p.Val188Met missense_variant 0.18
ribD 2986740 c.-99A>G upstream_gene_variant 0.25
ribD 2987573 c.735C>T synonymous_variant 0.17
ribD 2987612 c.774C>T synonymous_variant 0.17
Rv2752c 3064822 p.Val457Ala missense_variant 0.29
Rv2752c 3064828 p.Gly455Asp missense_variant 0.29
Rv2752c 3065067 c.1125C>T synonymous_variant 0.12
Rv2752c 3065485 p.Ala236Val missense_variant 0.25
Rv2752c 3065663 p.Pro177Ser missense_variant 0.12
thyA 3073866 c.606C>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087293 c.474G>T synonymous_variant 0.29
ald 3087330 p.Val171Ile missense_variant 0.33
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.45
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449441 p.Ala313Val missense_variant 0.12
Rv3083 3449779 p.Ala426Thr missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474015 c.9C>T synonymous_variant 0.29
fprA 3474082 p.Ala26Thr missense_variant 0.29
fprA 3474377 p.Ala124Val missense_variant 0.13
fprA 3474389 p.Phe128Ser missense_variant 0.11
fprA 3474526 p.Ala174Thr missense_variant 0.17
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474901 p.Ser299Arg missense_variant 0.4
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
whiB7 3568524 c.156C>T synonymous_variant 0.12
Rv3236c 3612432 p.Val229Met missense_variant 0.12
Rv3236c 3612682 c.435C>T synonymous_variant 0.5
Rv3236c 3612716 p.Ala134Val missense_variant 0.14
Rv3236c 3612772 c.345T>A synonymous_variant 0.14
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640724 p.Asp61Val missense_variant 0.22
fbiA 3640804 p.Ala88Ser missense_variant 0.13
fbiA 3640948 p.Trp136Arg missense_variant 0.25
fbiA 3640972 p.Pro144Ser missense_variant 0.13
fbiB 3641397 c.-138G>A upstream_gene_variant 0.18
fbiB 3641469 c.-66G>A upstream_gene_variant 0.12
fbiB 3642028 p.Val165Gly missense_variant 0.4
fbiB 3642687 c.1153C>T synonymous_variant 0.13
alr 3840397 p.Cys342Arg missense_variant 0.14
rpoA 3877737 c.771G>A synonymous_variant 0.18
rpoA 3877900 p.Ser203Asn missense_variant 0.12
rpoA 3878649 c.-142T>A upstream_gene_variant 0.25
clpC1 4038822 p.Glu628Gly missense_variant 0.11
clpC1 4038999 p.Phe569Tyr missense_variant 0.13
clpC1 4040089 p.Arg206Trp missense_variant 0.13
clpC1 4040357 c.348T>C synonymous_variant 0.29
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044158 p.Glu42Lys missense_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240953 p.Ile364Thr missense_variant 0.13
embC 4240992 p.Ala377Val missense_variant 0.4
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241683 c.1821G>A synonymous_variant 0.2
embC 4241701 p.Met613Ile missense_variant 0.17
embC 4242128 c.2266C>T synonymous_variant 0.17
embA 4242265 c.-968A>G upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243607 c.375G>A synonymous_variant 0.2
embA 4243681 p.Ala150Val missense_variant 0.2
embA 4244084 c.852C>T synonymous_variant 0.15
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244889 p.Ile553Phe missense_variant 0.4
embB 4245686 c.-828G>C upstream_gene_variant 0.4
embA 4245750 p.Met840Val missense_variant 0.15
embB 4245908 c.-606G>A upstream_gene_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246194 p.Pro988Ser missense_variant 0.14
embA 4246311 p.Gly1027Ser missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246563 p.Leu17Trp missense_variant 0.36
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247667 p.Trp385* stop_gained 0.67
embB 4247973 p.Thr487Ile missense_variant 0.14
embB 4248747 p.Gly745Val missense_variant 0.25
embB 4248752 p.Cys747Arg missense_variant 0.25
embB 4248857 p.Gly782Arg missense_variant 0.33
embB 4248872 p.Gly787Ser missense_variant 0.18
embB 4248919 c.2406C>T synonymous_variant 0.2
embB 4249617 p.Gly1035Asp missense_variant 0.13
embB 4249687 c.3174C>T synonymous_variant 0.18
aftB 4267172 c.1665C>T synonymous_variant 0.13
aftB 4267393 p.Pro482Ser missense_variant 0.25
aftB 4267401 p.Ala479Gly missense_variant 0.29
aftB 4267517 c.1320A>G synonymous_variant 0.17
aftB 4268089 p.Trp250Arg missense_variant 0.11
aftB 4268148 p.Gly230Val missense_variant 0.18
aftB 4268703 p.Asn45Ile missense_variant 0.12
ubiA 4268944 c.889delG frameshift_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269641 p.Ala65Thr missense_variant 0.2
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4269875 c.-42G>A upstream_gene_variant 0.18
ethA 4326108 p.Arg456Cys missense_variant 0.12
ethA 4327608 c.-135C>T upstream_gene_variant 0.22
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338440 p.Glu28Lys missense_variant 0.14
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 4407808 p.Asp132Gly missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407945 c.258C>T synonymous_variant 0.2