TB-Profiler result

Run: ERR4817976
Summary

Run ID: ERR4817976

Sample name:

Date: 01-04-2023 15:17:53

Number of reads: 928843

Percentage reads mapped: 57.48

Strain: lineage4.1.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.91 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6828 p.Met530Thr missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9428 p.Asp709Glu missense_variant 0.22
fgd1 491397 p.Glu205Asp missense_variant 0.15
fgd1 491506 p.Ala242Ser missense_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761027 c.1221A>G synonymous_variant 0.14
rpoB 762202 p.Lys799Met missense_variant 0.14
rpoB 762214 c.2411delG frameshift_variant 0.13
rpoC 764713 c.1344G>C synonymous_variant 0.11
rpoC 764716 c.1347G>C synonymous_variant 0.11
rpoC 764721 p.Leu451Pro missense_variant 0.11
rpoC 764737 c.1368G>C synonymous_variant 0.1
rpoC 764740 p.Met457Ile missense_variant 0.11
rpoC 764746 c.1377G>T synonymous_variant 0.11
rpoC 764762 p.His465Tyr missense_variant 0.11
rpoC 764776 p.Ile469Met missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775819 p.Phe888Leu missense_variant 0.14
mmpL5 776086 p.Val799Ile missense_variant 0.15
mmpL5 776617 p.Pro622Ser missense_variant 0.15
mmpL5 777714 p.Ile256Thr missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800804 c.-5G>T upstream_gene_variant 0.17
rplC 801363 c.555C>T synonymous_variant 0.13
fbiC 1302870 c.-61G>A upstream_gene_variant 0.2
embR 1416914 p.Trp145* stop_gained 0.12
atpE 1461153 p.Ser37Pro missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472096 n.251T>A non_coding_transcript_exon_variant 0.67
rrs 1472100 n.255T>C non_coding_transcript_exon_variant 0.67
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.6
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.33
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.29
rrs 1472118 n.273A>T non_coding_transcript_exon_variant 0.29
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.43
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.57
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.67
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.67
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.38
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.29
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.38
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.67
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.83
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 1.0
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.91
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.93
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.98
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.99
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.99
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.99
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.99
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.99
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.63
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.94
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 1.0
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 1.0
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.9
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.9
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.9
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.1
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.85
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.85
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.86
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.69
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.92
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.33
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.67
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.62
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.75
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 1.0
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 1.0
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 1.0
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 1.0
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 1.0
rrl 1474783 n.1126G>T non_coding_transcript_exon_variant 1.0
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.5
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.75
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 1.0
rrl 1474832 n.1175A>G non_coding_transcript_exon_variant 0.67
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 1.0
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 1.0
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 1.0
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 1.0
rrl 1475772 n.2115A>C non_coding_transcript_exon_variant 0.8
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 1.0
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.43
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.43
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.43
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.38
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.29
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.29
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.25
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.29
rrl 1475938 n.2281C>A non_coding_transcript_exon_variant 0.25
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.29
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.29
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.29
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.71
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.29
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.71
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.2
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.17
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.67
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.67
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.75
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.8
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.62
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.57
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.5
rrl 1476520 n.2863G>T non_coding_transcript_exon_variant 0.5
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.5
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.5
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.5
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.5
rrl 1476539 n.2882A>C non_coding_transcript_exon_variant 0.5
rrl 1476544 n.2887T>C non_coding_transcript_exon_variant 0.6
rrl 1476547 n.2890C>A non_coding_transcript_exon_variant 0.6
rrl 1476563 n.2906G>T non_coding_transcript_exon_variant 0.67
rrl 1476566 n.2909A>G non_coding_transcript_exon_variant 0.67
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.67
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.8
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.8
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.8
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.8
rrl 1476600 n.2943A>C non_coding_transcript_exon_variant 0.4
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.8
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.67
rrl 1476608 n.2951C>T non_coding_transcript_exon_variant 0.67
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.57
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.57
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.5
rrl 1476629 n.2972C>G non_coding_transcript_exon_variant 0.33
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.25
fabG1 1673987 p.Pro183Leu missense_variant 0.18
fabG1 1674061 p.Ala208Ser missense_variant 0.15
rpsA 1833363 c.-179A>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154166 p.Ala649Val missense_variant 0.12
PPE35 2168467 p.Leu716Phe missense_variant 0.2
PPE35 2170578 p.Ser12Leu missense_variant 0.12
Rv1979c 2222216 p.Val317Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289023 c.219C>T synonymous_variant 0.14
pncA 2289783 c.-542G>A upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087622 p.Ala268Gly missense_variant 0.14
ald 3087638 c.819C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877558 p.Pro317His missense_variant 0.12
rpoA 3877718 p.Leu264Ile missense_variant 0.14
rpoA 3878307 c.201C>A synonymous_variant 0.13
rpoA 3878527 c.-20C>A upstream_gene_variant 0.4
ddn 3987205 p.Glu121Gly missense_variant 0.1
clpC1 4038588 p.Arg706His missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4266961 p.Arg626Trp missense_variant 0.14
ubiA 4269158 p.Ala226Ser missense_variant 0.12
ethA 4327367 p.Glu36Val missense_variant 0.12
ethA 4327482 c.-9C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0