TB-Profiler result

Run: ERR5908213
Summary

Run ID: ERR5908213

Sample name:

Date: 02-04-2023 00:53:39

Number of reads: 1041548

Percentage reads mapped: 26.9

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
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 6089 p.Gly284Trp missense_variant 0.12
gyrB 6555 p.Pro439His missense_variant 0.18
gyrA 6784 c.-518C>T upstream_gene_variant 0.12
gyrB 6962 p.Arg575Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8127 p.Tyr276Asn missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491580 c.798C>T synonymous_variant 0.2
fgd1 491607 c.825G>T synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.24
mshA 576111 p.Ala255Gly missense_variant 0.24
rpoB 759798 c.-9G>A upstream_gene_variant 0.12
rpoB 759892 p.Ala29Glu missense_variant 0.14
rpoB 759901 p.Arg32Leu missense_variant 0.14
rpoB 760943 c.1137C>A synonymous_variant 0.12
rpoC 762863 c.-507T>C upstream_gene_variant 0.12
rpoB 762872 p.Met1022Ile missense_variant 0.12
rpoB 762878 p.Ile1024Met missense_variant 0.11
rpoC 762899 c.-471G>C upstream_gene_variant 0.16
rpoC 762905 c.-465C>T upstream_gene_variant 0.16
rpoB 762925 p.Thr1040Ile missense_variant 0.14
rpoC 762929 c.-441G>C upstream_gene_variant 0.14
rpoB 762939 p.Met1045Leu missense_variant 0.15
rpoC 762965 c.-405T>C upstream_gene_variant 0.15
rpoC 762980 c.-390T>C upstream_gene_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776108 p.Met791Ile missense_variant 0.15
mmpL5 776662 p.Leu607Ile missense_variant 0.11
mmpL5 776842 p.Ala547Ser missense_variant 0.11
mmpL5 778084 p.Pro133Ser missense_variant 0.12
mmpL5 779466 c.-986C>T upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800750 c.-59G>T upstream_gene_variant 0.12
rplC 800777 c.-32C>T upstream_gene_variant 0.17
rplC 800789 c.-20G>T upstream_gene_variant 0.17
Rv1258c 1406734 p.Ser203Thr missense_variant 0.13
atpE 1461100 p.Gly19Val missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472120 n.275G>A non_coding_transcript_exon_variant 0.18
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.57
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.57
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.53
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.53
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.38
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.38
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.27
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.15
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.37
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.35
rrs 1472349 n.504A>T non_coding_transcript_exon_variant 0.41
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.48
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.46
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.46
rrs 1472390 n.545T>C non_coding_transcript_exon_variant 0.5
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.55
rrs 1472432 n.587C>T non_coding_transcript_exon_variant 0.14
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.36
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.55
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.36
rrs 1472731 n.886C>T non_coding_transcript_exon_variant 0.2
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.55
rrs 1472737 n.892C>A non_coding_transcript_exon_variant 0.15
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.57
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.57
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.42
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.32
rrs 1472801 n.956G>T non_coding_transcript_exon_variant 0.14
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.29
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.29
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.15
rrs 1472968 n.1123C>A non_coding_transcript_exon_variant 0.12
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.12
rrs 1473012 n.1167G>T non_coding_transcript_exon_variant 0.13
rrs 1473082 n.1237G>T non_coding_transcript_exon_variant 0.25
rrs 1473227 n.1382C>T non_coding_transcript_exon_variant 0.17
rrl 1473425 n.-233G>T upstream_gene_variant 0.12
rrl 1474078 n.421G>A non_coding_transcript_exon_variant 0.5
rrl 1474184 n.528delG non_coding_transcript_exon_variant 0.22
rrl 1474495 n.838G>C non_coding_transcript_exon_variant 0.2
rrl 1474598 n.941C>T non_coding_transcript_exon_variant 0.2
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.17
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.17
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.17
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.27
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.42
rrl 1475833 n.2176A>G non_coding_transcript_exon_variant 0.11
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.5
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.5
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.44
rrl 1475894 n.2237C>G non_coding_transcript_exon_variant 0.25
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.25
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.41
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.41
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.41
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.61
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.61
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.68
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.77
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.81
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.85
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.85
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.85
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.82
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.82
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.74
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.74
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.77
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.77
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.72
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.76
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.76
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.76
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.61
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.54
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.53
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.53
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.47
rrl 1476521 n.2864C>T non_coding_transcript_exon_variant 0.47
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.47
rrl 1476525 n.2868A>C non_coding_transcript_exon_variant 0.47
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.47
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.47
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.47
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.47
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.47
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.53
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.42
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.42
rpsA 1833480 c.-62G>T upstream_gene_variant 0.17
rpsA 1833588 p.Ile16Thr missense_variant 0.18
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102886 p.Pro53Ser missense_variant 0.11
katG 2154033 c.2079C>T synonymous_variant 0.17
katG 2154249 c.1863C>A synonymous_variant 0.14
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156221 c.-110C>A upstream_gene_variant 0.15
katG 2156299 c.-188G>T upstream_gene_variant 0.29
PPE35 2168916 p.Pro566Leu missense_variant 0.29
PPE35 2168921 c.1692G>A synonymous_variant 0.22
PPE35 2169686 c.927T>C synonymous_variant 0.18
PPE35 2169689 c.924C>A synonymous_variant 0.18
Rv1979c 2222006 p.Ile387Val missense_variant 0.11
Rv1979c 2222877 c.288C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518225 c.111G>A synonymous_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
pepQ 2859429 c.989delT frameshift_variant 0.12
Rv2752c 3065984 c.208C>A synonymous_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449683 p.Ser394Pro missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038441 p.Ala755Val missense_variant 0.14
embC 4242005 p.Leu715Met missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269448 p.Val129Ala missense_variant 0.15
ethA 4326149 p.Ser442Leu missense_variant 0.17
ethA 4327298 p.Met59Thr missense_variant 0.18
whiB6 4338518 c.4C>A synonymous_variant 0.12
whiB6 4338562 c.-41C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
Rv2752c 3065039 c.1070_1152delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT frameshift_variant 1.0