TB-Profiler result

Run: ERR4828388
Summary

Run ID: ERR4828388

Sample name:

Date: 01-04-2023 18:51:35

Number of reads: 3214696

Percentage reads mapped: 88.73

Strain: lineage1.1.1

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 0.98
lineage1.1.1 Indo-Oceanic EAI4;EAI5 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 2154798 p.Trp438* stop_gained 0.4 isoniazid
ethA 4326858 p.Gln206* stop_gained 0.29 ethionamide
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 5053 c.-187C>T upstream_gene_variant 0.25
gyrB 6014 p.Asp259Asn missense_variant 0.17
gyrB 6048 p.Ala270Glu missense_variant 0.15
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6267 p.Pro343His missense_variant 0.29
gyrB 6582 p.Thr448Met missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8169 p.Gln290Lys missense_variant 0.22
gyrA 8349 p.Asp350Tyr missense_variant 0.4
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8490 p.Ala397Ser missense_variant 0.25
gyrA 8507 c.1206C>T synonymous_variant 0.29
gyrA 8823 p.Glu508* stop_gained 0.2
gyrA 8850 p.Val517Ile missense_variant 0.2
gyrA 8940 p.Ala547Thr missense_variant 0.22
gyrA 9039 p.Lys580* stop_gained 0.29
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9663 p.Ala788Ser missense_variant 0.29
fgd1 490972 p.Arg64Ser missense_variant 1.0
fgd1 491496 c.714C>T synonymous_variant 0.27
fgd1 491523 c.741G>T synonymous_variant 0.15
fgd1 491607 c.825G>A synonymous_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575509 c.162C>A synonymous_variant 0.33
mshA 575903 p.Ala186Thr missense_variant 0.67
mshA 575991 p.Val215Asp missense_variant 0.4
mshA 576073 c.726C>T synonymous_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.43
ccsA 619723 c.-168G>A upstream_gene_variant 0.33
ccsA 620056 p.Thr56Pro missense_variant 0.25
ccsA 620301 c.411G>T synonymous_variant 0.67
rpoB 760861 p.Pro352Leu missense_variant 0.33
rpoB 761015 c.1209G>C synonymous_variant 0.67
rpoB 761780 c.1974C>T synonymous_variant 0.22
rpoC 762503 c.-867G>A upstream_gene_variant 0.4
rpoC 762821 c.-549C>T upstream_gene_variant 0.2
rpoC 763835 p.Ala156Thr missense_variant 0.22
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764075 p.Val236Phe missense_variant 0.5
rpoC 764202 p.Arg278Leu missense_variant 0.4
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765225 p.Ile619Asn missense_variant 0.5
rpoC 765253 p.Ser628Arg missense_variant 1.0
rpoC 765653 p.Arg762Cys missense_variant 0.4
rpoC 765740 p.Glu791Lys missense_variant 0.4
rpoC 766055 p.Gly896Cys missense_variant 0.67
rpoC 766118 p.Glu917Lys missense_variant 1.0
rpoC 766564 c.3195C>A synonymous_variant 0.67
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776180 c.2301C>T synonymous_variant 0.4
mmpL5 776398 p.Val695Ile missense_variant 0.33
mmpL5 776494 p.Gln663Lys missense_variant 0.4
mmpL5 776604 p.Arg626Leu missense_variant 0.2
mmpL5 776819 c.1662C>A synonymous_variant 0.25
mmpL5 776899 p.Asp528Asn missense_variant 0.29
mmpL5 777209 c.1272C>T synonymous_variant 0.22
mmpL5 777422 c.1059G>T synonymous_variant 0.5
mmpL5 777527 c.954G>T synonymous_variant 0.25
mmpL5 777581 p.Tyr300* stop_gained 1.0
mmpL5 778229 p.Glu84Asp missense_variant 0.5
mmpL5 778563 c.-83C>A upstream_gene_variant 0.33
mmpL5 778618 c.-138G>A upstream_gene_variant 0.4
mmpS5 778792 p.Leu38Phe missense_variant 0.4
mmpR5 779317 p.Ala110Thr missense_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781808 c.249C>T synonymous_variant 0.4
rplC 800841 c.33G>T synonymous_variant 0.22
rplC 800850 c.42G>T synonymous_variant 0.22
rplC 801441 c.633G>A synonymous_variant 0.2
fbiC 1303144 p.Ser72Ala missense_variant 0.43
fbiC 1303197 p.Lys89Asn missense_variant 0.29
fbiC 1303525 p.Ser199Thr missense_variant 0.18
fbiC 1303553 p.Ala208Val missense_variant 0.22
fbiC 1303600 p.Glu224* stop_gained 0.22
fbiC 1303647 c.717G>A synonymous_variant 0.25
fbiC 1303792 p.Gln288* stop_gained 0.18
fbiC 1304040 c.1110C>A synonymous_variant 0.33
fbiC 1304258 p.Ser443Tyr missense_variant 0.5
fbiC 1304740 p.Gly604Ser missense_variant 0.4
embR 1416610 c.738G>T synonymous_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461068 c.24C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473174 n.1329G>A non_coding_transcript_exon_variant 0.25
rrs 1473243 n.1398G>A non_coding_transcript_exon_variant 0.33
rrl 1473640 n.-18C>T upstream_gene_variant 0.22
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.33
rrl 1474202 n.545T>A non_coding_transcript_exon_variant 0.33
rrl 1474641 n.984G>A non_coding_transcript_exon_variant 0.4
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1474905 n.1248T>A non_coding_transcript_exon_variant 0.4
rrl 1474979 n.1322G>A non_coding_transcript_exon_variant 0.33
fabG1 1673469 c.35delC frameshift_variant 0.4
fabG1 1673782 p.Gly115Trp missense_variant 0.29
inhA 1674303 c.102C>T synonymous_variant 0.5
inhA 1674621 c.420C>A synonymous_variant 0.33
rpsA 1833533 c.-9C>T upstream_gene_variant 0.25
rpsA 1833562 c.21C>T synonymous_variant 0.18
rpsA 1834319 p.Val260Ile missense_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918045 p.Gly36Trp missense_variant 0.4
tlyA 1918081 p.Asp48Asn missense_variant 0.4
ndh 2101717 c.1326C>A synonymous_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155816 p.Gly99Val missense_variant 0.5
katG 2156019 p.Glu31Asp missense_variant 0.25
katG 2156312 c.-201G>T upstream_gene_variant 0.4
katG 2156389 c.-278G>C upstream_gene_variant 1.0
PPE35 2167682 c.2931G>T synonymous_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168301 p.Thr771Ile missense_variant 0.2
PPE35 2168628 p.Ile662Thr missense_variant 0.11
PPE35 2168778 p.Thr612Ile missense_variant 0.14
PPE35 2169263 c.1350C>T synonymous_variant 0.25
PPE35 2169465 p.Asn383Ile missense_variant 0.29
PPE35 2170018 p.Ala199Ser missense_variant 0.5
Rv1979c 2221943 c.1222C>A synonymous_variant 0.13
Rv1979c 2222154 c.1011G>T synonymous_variant 0.4
Rv1979c 2222223 c.942C>T synonymous_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289313 c.-72G>C upstream_gene_variant 0.29
pncA 2289322 c.-81C>A upstream_gene_variant 0.29
pncA 2289719 c.-478G>T upstream_gene_variant 0.15
pncA 2290207 c.-966G>A upstream_gene_variant 0.22
pncA 2290219 c.-978C>T upstream_gene_variant 0.25
kasA 2517951 c.-164G>A upstream_gene_variant 0.5
kasA 2517954 c.-161G>A upstream_gene_variant 0.67
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518166 p.Ala18Ser missense_variant 0.17
kasA 2519322 p.Gly403Glu missense_variant 0.4
eis 2714161 p.Ala391Val missense_variant 0.5
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726202 c.10C>T synonymous_variant 0.33
ahpC 2726726 p.Trp178* stop_gained 0.33
ahpC 2726755 p.Gly188Val missense_variant 0.22
folC 2746265 p.Ser445Leu missense_variant 0.67
folC 2746675 c.924C>T synonymous_variant 0.22
pepQ 2859569 p.Ala284Ser missense_variant 0.29
pepQ 2860366 p.Gly18Val missense_variant 0.4
ribD 2986991 c.153C>T synonymous_variant 0.33
ribD 2987036 c.198C>A synonymous_variant 0.2
ribD 2987495 c.657C>T synonymous_variant 0.5
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064773 c.1419C>T synonymous_variant 0.5
Rv2752c 3065156 p.Glu346Lys missense_variant 0.5
Rv2752c 3065581 p.Thr204Lys missense_variant 0.29
Rv2752c 3065750 p.His148Asn missense_variant 0.33
thyX 3067300 c.646C>T synonymous_variant 0.4
thyX 3067601 c.345G>A synonymous_variant 0.29
thyX 3067686 p.Arg87Leu missense_variant 0.33
thyA 3073761 c.711A>G synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339421 p.Val102Leu missense_variant 0.67
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448911 c.408C>A synonymous_variant 1.0
Rv3083 3449138 p.Arg212Gln missense_variant 0.5
Rv3083 3449383 p.Asp294Tyr missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474368 p.Gly121Asp missense_variant 0.29
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474851 p.Arg282His missense_variant 0.67
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612521 p.Ser199Leu missense_variant 0.5
Rv3236c 3612609 p.Ala170Pro missense_variant 0.67
Rv3236c 3613047 p.Val24Met missense_variant 0.14
Rv3236c 3613186 c.-70G>T upstream_gene_variant 0.2
fbiA 3640364 c.-179G>T upstream_gene_variant 0.33
fbiA 3640402 c.-141C>A upstream_gene_variant 0.22
fbiB 3640545 c.-990G>A upstream_gene_variant 0.4
fbiA 3640801 p.His87Tyr missense_variant 1.0
fbiB 3641490 c.-45G>A upstream_gene_variant 0.25
fbiB 3641878 p.Arg115Gln missense_variant 0.22
fbiB 3642534 c.1000C>A synonymous_variant 1.0
fbiB 3642604 p.Ala357Val missense_variant 0.67
fbiB 3642801 p.Ala423Thr missense_variant 0.33
alr 3840603 p.Pro273Leu missense_variant 0.25
alr 3841316 c.105C>T synonymous_variant 0.5
alr 3841364 c.57C>T synonymous_variant 0.5
alr 3841610 c.-190C>A upstream_gene_variant 0.4
rpoA 3877635 c.873G>A synonymous_variant 0.2
rpoA 3877790 p.Glu240Lys missense_variant 0.5
rpoA 3878185 p.Gly108Asp missense_variant 0.2
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3986694 c.-150G>T upstream_gene_variant 0.4
clpC1 4039572 p.Ala378Glu missense_variant 0.29
clpC1 4040143 p.Asp188Asn missense_variant 0.13
clpC1 4040212 p.Pro165Ser missense_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4043986 p.Arg99His missense_variant 0.22
panD 4044180 c.102C>T synonymous_variant 0.2
panD 4044334 c.-53A>T upstream_gene_variant 0.18
embC 4239849 c.-14C>A upstream_gene_variant 0.67
embC 4240329 p.Thr156Ile missense_variant 0.25
embC 4240441 p.Phe193Leu missense_variant 0.25
embC 4240932 p.Trp357* stop_gained 1.0
embC 4242029 p.Leu723Met missense_variant 0.4
embA 4243457 c.225C>A synonymous_variant 0.25
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244056 p.Gly275Val missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247033 p.Ser174Arg missense_variant 0.4
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249696 p.Trp1061Cys missense_variant 0.25
aftB 4267364 p.Met491Ile missense_variant 0.4
aftB 4268076 p.Met254Lys missense_variant 0.33
aftB 4268452 p.Pro129Ser missense_variant 0.33
aftB 4268500 p.Arg113Cys missense_variant 0.5
aftB 4268619 p.Val73Gly missense_variant 0.23
aftB 4268623 p.Trp72Gly missense_variant 0.23
aftB 4268638 p.Leu67Val missense_variant 0.29
aftB 4269180 c.-344G>A upstream_gene_variant 0.5
ubiA 4269266 p.Gly190Cys missense_variant 0.5
aftB 4269320 c.-484C>T upstream_gene_variant 0.25
aftB 4269342 c.-506G>T upstream_gene_variant 0.5
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326364 p.Lys370Asn missense_variant 0.2
ethR 4327722 p.Arg58Ser missense_variant 0.33
ethR 4327846 p.Glu100Lys missense_variant 0.22
ethA 4327911 c.-438G>T upstream_gene_variant 0.33
ethR 4327961 p.Trp138* stop_gained 0.5
ethR 4328005 p.Ile153Val missense_variant 1.0
ethR 4328045 p.Leu166Arg missense_variant 0.3
whiB6 4338242 p.Gln94Glu missense_variant 0.8
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407575 p.Gln210Lys missense_variant 0.18
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408098 c.105G>A synonymous_variant 0.33
gid 4408101 c.102G>A synonymous_variant 0.33
gid 4408139 p.Tyr22His missense_variant 1.0
gid 4408153 p.Gly17Ala missense_variant 0.29
gid 4408360 c.-158C>T upstream_gene_variant 0.17
gid 4408363 c.-161G>A upstream_gene_variant 0.15
gid 4408460 c.-258G>T upstream_gene_variant 0.25