TB-Profiler result

Run: SRR4034769
Summary

Run ID: SRR4034769

Sample name:

Date: 04-04-2023 07:03:56

Number of reads: 964124

Percentage reads mapped: 27.65

Strain: lineage4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.92
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
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 5224 c.-15_-14delGA upstream_gene_variant 0.25
gyrB 7164 p.Ala642Asp missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7459 p.Arg53Leu missense_variant 0.22
gyrA 7499 c.198G>A synonymous_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7657 p.Pro119Leu missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9320 c.2019G>C synonymous_variant 0.17
fgd1 491285 p.Gly168Val missense_variant 0.29
fgd1 491342 p.Arg187His missense_variant 0.8
rpoB 759817 p.Ser4Tyr missense_variant 0.17
rpoB 760452 p.Val216Ile missense_variant 0.15
rpoB 761062 p.Ala419Val missense_variant 0.67
rpoB 761122 p.Pro439Gln missense_variant 0.5
rpoB 762120 p.Asp772Asn missense_variant 0.22
rpoB 762837 p.Glu1011* stop_gained 0.22
rpoC 763381 c.12C>G synonymous_variant 0.17
rpoC 763606 c.237C>T synonymous_variant 0.18
rpoC 764219 p.Gly284Ser missense_variant 0.25
rpoC 764331 p.Pro321Gln missense_variant 0.25
rpoC 764534 p.Arg389Trp missense_variant 0.17
rpoC 764611 c.1242G>T synonymous_variant 0.22
rpoC 764620 c.1251G>T synonymous_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 0.83
rpoC 765323 p.Gly652Ser missense_variant 0.25
rpoC 765580 c.2211G>A synonymous_variant 0.33
rpoC 765838 c.2469G>A synonymous_variant 0.2
rpoC 765885 p.Ser839Tyr missense_variant 0.18
rpoC 766625 p.Leu1086Met missense_variant 0.4
rpoC 766861 c.3492G>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776041 p.Ala814Thr missense_variant 0.29
mmpL5 776345 c.2136C>T synonymous_variant 0.2
mmpS5 778568 p.Thr113Asn missense_variant 0.14
mmpR5 779375 p.Pro129Leu missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781717 p.Ala53Asp missense_variant 0.29
rpsL 781927 c.371delG frameshift_variant 0.29
rplC 800717 c.-92C>A upstream_gene_variant 0.14
fbiC 1302757 c.-173_-168delATCGCG upstream_gene_variant 0.2
fbiC 1302891 c.-40G>T upstream_gene_variant 0.25
fbiC 1304067 c.1137G>C synonymous_variant 0.15
Rv1258c 1406143 p.Leu400Met missense_variant 0.18
Rv1258c 1407035 p.Asn102Lys missense_variant 0.5
embR 1416428 p.Ala307Glu missense_variant 0.29
embR 1416520 c.828G>A synonymous_variant 0.25
embR 1416688 c.660G>A synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471671 n.-175G>T upstream_gene_variant 0.17
rrs 1471776 n.-70G>A upstream_gene_variant 0.14
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.2
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.15
rrs 1472078 n.233C>A non_coding_transcript_exon_variant 0.18
rrs 1472079 n.234C>A non_coding_transcript_exon_variant 0.18
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.2
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.18
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.18
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.54
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.54
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.74
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.72
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.71
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.71
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.72
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.72
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.73
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.31
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.15
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.69
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.8
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.91
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.9
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.86
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.84
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.81
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.3
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.18
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.22
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.23
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.33
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.36
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.41
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.48
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.47
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.15
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.15
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.45
rrl 1473533 n.-125G>T upstream_gene_variant 0.18
rrl 1474289 n.636delT non_coding_transcript_exon_variant 0.13
rrl 1474302 n.645G>A non_coding_transcript_exon_variant 0.12
rrl 1474789 n.1132G>T non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.18
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.22
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.29
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.25
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.22
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.31
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.31
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.27
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.27
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.24
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.24
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.29
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.33
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.33
rrl 1475688 n.2031G>C non_coding_transcript_exon_variant 0.33
rrl 1475692 n.2035G>A non_coding_transcript_exon_variant 0.33
rrl 1475695 n.2038G>A non_coding_transcript_exon_variant 0.33
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.29
rrl 1475704 n.2047C>T non_coding_transcript_exon_variant 0.29
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.29
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.22
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.17
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.53
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.57
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.58
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.65
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.63
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.52
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.55
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.15
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.15
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.25
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.35
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.2
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.43
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.43
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.43
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.86
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.89
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.9
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.93
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.95
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.96
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.95
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.94
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.93
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.93
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.87
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.82
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.79
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.78
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.77
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.81
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.74
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.74
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.74
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.74
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.74
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.78
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.85
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.74
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.69
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.69
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.69
inhA 1674859 p.Glu220* stop_gained 0.25
rpsA 1833438 c.-104C>A upstream_gene_variant 0.4
rpsA 1833633 c.93_94dupGT frameshift_variant 0.22
rpsA 1834110 p.Trp190* stop_gained 0.2
rpsA 1834379 p.Gln280* stop_gained 0.25
rpsA 1834444 c.903C>A synonymous_variant 0.4
rpsA 1834665 p.Pro375Gln missense_variant 0.12
rpsA 1834732 p.Asp397Glu missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918653 c.714G>A synonymous_variant 0.14
ndh 2102397 p.Ala216Ser missense_variant 0.17
katG 2154103 p.Pro670His missense_variant 0.4
katG 2154489 c.1623C>T synonymous_variant 0.29
katG 2154596 p.Glu506* stop_gained 0.25
katG 2155304 p.His270Asn missense_variant 0.33
katG 2155599 c.513C>T synonymous_variant 0.25
katG 2155706 p.Pro136Ser missense_variant 0.25
PPE35 2168090 c.2523C>A synonymous_variant 0.2
PPE35 2168504 c.2109C>A synonymous_variant 0.14
PPE35 2169295 p.Gly440Ser missense_variant 0.14
PPE35 2170553 c.60C>A synonymous_variant 0.21
PPE35 2170617 c.-5G>A upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223312 c.-148C>A upstream_gene_variant 0.14
pncA 2289161 c.81G>T synonymous_variant 0.15
pncA 2289897 c.-656G>T upstream_gene_variant 0.18
pncA 2289979 c.-738G>T upstream_gene_variant 0.17
kasA 2518719 p.Ile202Asn missense_variant 0.4
eis 2714871 c.462G>T synonymous_variant 0.25
eis 2715198 c.135G>A synonymous_variant 0.5
eis 2715209 c.123dupC frameshift_variant 0.5
ahpC 2725941 c.-252C>T upstream_gene_variant 0.17
ahpC 2726010 c.-183G>A upstream_gene_variant 0.14
ahpC 2726690 c.498C>T synonymous_variant 0.25
folC 2747327 p.Arg91Leu missense_variant 0.22
folC 2747789 c.-191G>T upstream_gene_variant 0.25
pepQ 2859883 p.Leu179Pro missense_variant 0.33
ribD 2986907 c.69C>A synonymous_variant 1.0
ribD 2987154 c.316C>A synonymous_variant 0.33
Rv2752c 3065433 c.759G>T synonymous_variant 0.22
Rv2752c 3065544 p.Ser216Arg missense_variant 0.17
Rv2752c 3065573 p.Glu207* stop_gained 0.29
Rv2752c 3066282 c.-91G>A upstream_gene_variant 0.25
thyX 3067588 p.Pro120Thr missense_variant 0.29
thyX 3067663 p.Arg95Ser missense_variant 0.25
thyX 3067831 p.Ala39Ser missense_variant 0.2
thyA 3074212 p.Thr87Ile missense_variant 0.5
ald 3086780 c.-40T>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087483 p.Ala222Ser missense_variant 0.17
fbiD 3338942 c.-176G>T upstream_gene_variant 0.5
fbiD 3339051 c.-67C>A upstream_gene_variant 0.4
fbiD 3339223 p.Glu36* stop_gained 0.33
fbiD 3339455 p.Leu113Pro missense_variant 0.67
Rv3083 3449090 p.Met196Thr missense_variant 0.22
Rv3083 3449418 c.915G>A synonymous_variant 0.29
Rv3083 3449744 p.Ala414Val missense_variant 0.29
Rv3083 3449790 c.1287C>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474039 c.33C>A synonymous_variant 0.5
fprA 3474598 p.Gly198Trp missense_variant 0.25
fprA 3474764 p.Arg253His missense_variant 0.2
fprA 3475167 c.1161C>T synonymous_variant 1.0
Rv3236c 3612390 p.Gly243Cys missense_variant 0.18
Rv3236c 3612688 c.429C>A synonymous_variant 0.15
Rv3236c 3612847 c.270G>A synonymous_variant 0.29
Rv3236c 3613150 c.-34G>T upstream_gene_variant 0.33
fbiB 3640578 c.-957C>A upstream_gene_variant 0.2
fbiB 3640728 c.-807G>T upstream_gene_variant 0.2
fbiA 3641093 p.Ser184Ile missense_variant 0.29
fbiA 3641447 p.Thr302Met missense_variant 0.5
fbiB 3641589 p.Gly19Trp missense_variant 0.29
fbiB 3641848 p.Ala105Asp missense_variant 0.15
fbiB 3642463 p.Leu310Pro missense_variant 0.25
fbiB 3642672 c.1140delC frameshift_variant 0.25
alr 3840370 p.Gly351Cys missense_variant 0.22
alr 3840628 c.792delC frameshift_variant 0.22
alr 3840728 c.693G>T synonymous_variant 0.33
alr 3840731 p.Glu230Asp missense_variant 0.33
alr 3840754 p.Arg223Ser missense_variant 0.33
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3877664 p.Asp282Tyr missense_variant 0.22
rpoA 3877737 c.771G>A synonymous_variant 0.25
rpoA 3877889 p.Ala207Thr missense_variant 0.22
rpoA 3878210 p.Gln100* stop_gained 0.4
ddn 3986699 c.-145C>G upstream_gene_variant 0.22
clpC1 4038245 c.2460C>T synonymous_variant 1.0
clpC1 4038416 c.2289C>A synonymous_variant 0.5
clpC1 4038753 p.Gln651Leu missense_variant 0.33
embC 4239725 c.-138G>T upstream_gene_variant 0.67
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241209 c.1347G>A synonymous_variant 0.29
embC 4241515 c.1653G>A synonymous_variant 0.4
embC 4241661 c.1804delG frameshift_variant 0.29
embC 4241725 c.1863G>T synonymous_variant 0.15
embA 4242544 c.-689C>A upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.88
embA 4242895 c.-338C>A upstream_gene_variant 0.5
embA 4244362 c.1132_1134delGGC conservative_inframe_deletion 0.2
embA 4244707 p.Thr492Asn missense_variant 1.0
embA 4244977 p.Gly582Glu missense_variant 0.67
embA 4246404 p.Glu1058* stop_gained 0.25
embA 4246419 p.Leu1063Met missense_variant 0.22
embB 4249352 p.Arg947Trp missense_variant 0.15
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268191 p.Ala216Thr missense_variant 0.67
aftB 4268278 p.Pro187Thr missense_variant 0.33
ubiA 4269028 p.Gly269Val missense_variant 0.25
aftB 4269375 c.-539G>A upstream_gene_variant 0.33
ethA 4326654 p.Glu274Lys missense_variant 0.22
ethA 4327020 p.Ala152Ser missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338678 c.-157G>C upstream_gene_variant 0.13
gid 4408401 c.-199T>C upstream_gene_variant 0.17