TB-Profiler result

Run: ERR1750941
Summary

Run ID: ERR1750941

Sample name:

Date: 31-03-2023 15:01:28

Number of reads: 1463975

Percentage reads mapped: 95.3

Strain: lineage4.8;lineage4.1.2

Drug-resistance: Sensitive

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.84
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.11
lineage4.1.2 Euro-American T;H None 0.75
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
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 5444 p.Leu69Met missense_variant 0.13
gyrA 6922 c.-380G>T upstream_gene_variant 0.18
gyrB 6927 p.Leu563Trp missense_variant 0.2
gyrA 7347 p.Glu16Lys missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.47
gyrA 7610 p.Trp103* stop_gained 0.15
gyrA 7636 c.337delC frameshift_variant 0.17
gyrA 8055 p.Arg252Gly missense_variant 0.17
gyrA 8101 p.Thr267Asn missense_variant 0.25
gyrA 8823 p.Glu508* stop_gained 0.18
gyrA 9024 c.1723C>A synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 0.79
fgd1 490751 c.-32T>G upstream_gene_variant 0.33
fgd1 491433 c.651C>T synonymous_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 0.72
mshA 576317 p.Arg324Trp missense_variant 0.15
ccsA 620748 c.858T>G synonymous_variant 0.48
rpoB 760115 c.309C>T synonymous_variant 0.43
rpoB 760991 c.1185G>A synonymous_variant 0.22
rpoB 761963 c.2157G>A synonymous_variant 0.18
rpoB 762787 c.2982delG frameshift_variant 0.15
rpoC 763443 p.Tyr25Phe missense_variant 0.29
rpoC 764245 c.876C>A synonymous_variant 0.14
rpoC 764449 c.1080G>C synonymous_variant 0.13
rpoC 764453 p.Ala362Ser missense_variant 0.14
rpoC 764458 c.1089G>C synonymous_variant 0.14
rpoC 764461 c.1092A>G synonymous_variant 0.14
rpoC 764470 c.1101C>G synonymous_variant 0.13
rpoC 764497 c.1128A>G synonymous_variant 0.13
rpoC 764503 c.1134G>C synonymous_variant 0.12
rpoC 764549 p.Pro394Ser missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 0.64
rpoC 766236 p.Gly956Asp missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776006 p.His825Gln missense_variant 0.17
mmpL5 778321 p.Glu54Lys missense_variant 0.17
mmpS5 778903 c.3G>A start_lost 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303443 c.513G>A synonymous_variant 0.15
Rv1258c 1406318 c.1023A>G synonymous_variant 0.14
Rv1258c 1406368 p.Tyr325Asn missense_variant 0.18
Rv1258c 1406872 p.Gly157Ser missense_variant 0.2
embR 1416288 p.His354Asn missense_variant 0.15
atpE 1461101 c.57T>G synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472025 n.180A>T non_coding_transcript_exon_variant 0.29
rrs 1472115 n.270C>T non_coding_transcript_exon_variant 0.25
rrs 1473296 n.1451G>T non_coding_transcript_exon_variant 0.29
rrs 1473382 n.1537T>A splice_region_variant&non_coding_transcript_exon_variant 0.33
rrl 1473675 n.18C>A non_coding_transcript_exon_variant 0.29
rrl 1474408 n.751G>T non_coding_transcript_exon_variant 0.29
rrl 1474466 n.809G>A non_coding_transcript_exon_variant 0.29
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.33
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.33
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.33
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.33
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.33
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.33
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.29
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.33
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.5
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.5
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.29
rrl 1476451 n.2794C>T non_coding_transcript_exon_variant 0.5
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 1.0
inhA 1674092 c.-110C>G upstream_gene_variant 0.11
inhA 1674563 p.His121Leu missense_variant 0.18
rpsA 1833689 p.Glu50Lys missense_variant 0.22
rpsA 1833919 c.378C>T synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918371 c.432C>T synonymous_variant 0.15
ndh 2101769 p.Arg425Leu missense_variant 0.67
ndh 2101895 p.Gly383Val missense_variant 0.33
ndh 2101914 p.Ser377Thr missense_variant 0.29
ndh 2101961 p.Pro361Gln missense_variant 0.4
ndh 2101989 p.Ala352Thr missense_variant 0.29
ndh 2102540 p.Ala168Gly missense_variant 0.31
katG 2154126 c.1986C>A synonymous_variant 0.29
PPE35 2168080 p.Thr845Ser missense_variant 0.17
PPE35 2168104 p.Pro837Ser missense_variant 0.3
PPE35 2168149 p.Pro822Ser missense_variant 0.43
PPE35 2169149 c.1464G>C synonymous_variant 0.25
PPE35 2170783 c.-171A>T upstream_gene_variant 0.5
PPE35 2170784 c.-172A>G upstream_gene_variant 0.5
Rv1979c 2222141 p.Arg342Cys missense_variant 0.14
Rv1979c 2222962 p.Ala68Val missense_variant 0.25
Rv1979c 2223243 c.-79G>T upstream_gene_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288759 c.483G>A synonymous_variant 0.29
pncA 2289293 c.-52C>A upstream_gene_variant 0.17
pncA 2289406 c.-165G>T upstream_gene_variant 0.17
kasA 2518014 c.-101G>C upstream_gene_variant 0.29
kasA 2518076 c.-39C>T upstream_gene_variant 0.75
kasA 2518151 p.Ser13Arg missense_variant 0.25
kasA 2518418 p.Glu102* stop_gained 0.17
kasA 2519327 p.Gly405Ser missense_variant 0.2
eis 2714702 p.Asp211Asn missense_variant 0.15
eis 2715436 c.-104G>A upstream_gene_variant 1.0
ahpC 2725949 c.-244G>T upstream_gene_variant 0.2
ahpC 2726039 c.-153delG upstream_gene_variant 0.2
ahpC 2726043 c.-150C>A upstream_gene_variant 0.2
ahpC 2726229 p.Tyr13Asp missense_variant 0.13
ahpC 2726265 p.Lys25Gln missense_variant 0.33
ahpC 2726338 p.Val49Gly missense_variant 0.5
folC 2746174 c.1425A>G synonymous_variant 0.11
folC 2747169 p.Lys144* stop_gained 0.2
pepQ 2859552 c.867C>T synonymous_variant 0.14
pepQ 2859659 p.Ala254Thr missense_variant 0.14
pepQ 2859744 c.675G>A synonymous_variant 0.18
pepQ 2860356 c.63G>T synonymous_variant 0.29
pepQ 2860429 c.-11C>T upstream_gene_variant 0.14
pepQ 2860443 c.-25A>G upstream_gene_variant 0.12
Rv2752c 3065098 p.Asn365Ser missense_variant 0.33
Rv2752c 3065472 c.720C>A synonymous_variant 0.18
Rv2752c 3066025 p.Gly56Val missense_variant 0.22
Rv2752c 3066252 c.-61C>T upstream_gene_variant 0.18
thyA 3073869 p.Trp201Cys missense_variant 0.17
thyA 3074162 p.Pro104Ser missense_variant 0.17
thyA 3074201 p.Gly91Trp missense_variant 0.22
thyA 3074248 p.His75Leu missense_variant 0.2
thyA 3074408 p.Thr22Ser missense_variant 0.18
thyA 3074461 p.Tyr4Phe missense_variant 0.17
ald 3086713 c.-107C>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448391 c.-113C>T upstream_gene_variant 0.17
Rv3083 3448983 c.480C>A synonymous_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.67
fprA 3474398 p.Trp131* stop_gained 0.22
fprA 3474961 p.Val319Met missense_variant 0.2
fprA 3475240 p.Ala412Pro missense_variant 0.11
Rv3236c 3612263 p.Gly285Val missense_variant 0.2
fbiB 3641629 c.98_100delTCG disruptive_inframe_deletion 0.11
rpoA 3877940 p.Asp190Asn missense_variant 0.25
clpC1 4038923 c.1782A>G synonymous_variant 0.17
clpC1 4038926 c.1779G>T synonymous_variant 0.17
clpC1 4038941 c.1764G>C synonymous_variant 0.17
clpC1 4038944 c.1761C>T synonymous_variant 0.17
clpC1 4038953 c.1752A>G synonymous_variant 0.15
clpC1 4038956 c.1749T>C synonymous_variant 0.15
clpC1 4038965 c.1740T>C synonymous_variant 0.17
clpC1 4038971 c.1734T>C synonymous_variant 0.18
clpC1 4038974 c.1731T>C synonymous_variant 0.17
clpC1 4038980 c.1725C>T synonymous_variant 0.15
clpC1 4038986 p.Asp573Glu missense_variant 0.14
clpC1 4038989 c.1716T>C synonymous_variant 0.15
clpC1 4038997 c.1708T>C synonymous_variant 0.14
clpC1 4039004 c.1701C>G synonymous_variant 0.14
clpC1 4039019 c.1686G>C synonymous_variant 0.13
clpC1 4039022 c.1683A>G synonymous_variant 0.13
clpC1 4039071 p.Pro545Gln missense_variant 0.15
clpC1 4039073 c.1632C>T synonymous_variant 0.17
clpC1 4039108 p.Arg533Trp missense_variant 0.2
clpC1 4039729 p.Asp326Asn missense_variant 0.5
panD 4043994 c.288C>T synonymous_variant 0.33
panD 4044016 p.Ala89Val missense_variant 0.29
embC 4239735 c.-128C>T upstream_gene_variant 0.17
embC 4239950 c.88C>A synonymous_variant 0.17
embC 4240049 c.191delA frameshift_variant 0.22
embC 4241763 p.Phe634Tyr missense_variant 0.15
embC 4241783 p.Trp641Arg missense_variant 0.2
embC 4242222 p.Pro787His missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.92
embA 4245414 p.Thr728Ala missense_variant 0.11
embA 4246460 p.Glu1076Asp missense_variant 0.22
embA 4246489 p.Arg1086Gln missense_variant 0.18
embB 4249268 p.Asp919Asn missense_variant 0.18
embB 4249323 p.Ala937Glu missense_variant 0.25
aftB 4267114 c.1722delG frameshift_variant 0.4
aftB 4267251 p.Asp529Val missense_variant 0.29
aftB 4267421 c.1416C>A synonymous_variant 0.15
aftB 4267836 p.Met334Lys missense_variant 0.22
aftB 4268384 p.Leu151Phe missense_variant 0.59
ubiA 4269511 p.Val108Gly missense_variant 0.45
ubiA 4269765 c.68delC frameshift_variant 0.15
ubiA 4270009 c.-176C>T upstream_gene_variant 0.39
ethR 4326715 c.-834G>A upstream_gene_variant 0.22
ethA 4327213 p.Ser87Arg missense_variant 0.25
gid 4407539 p.Gly222Arg missense_variant 0.2
gid 4407731 c.472C>A synonymous_variant 0.2