TB-Profiler result

Run: ERR1750929
Summary

Run ID: ERR1750929

Sample name:

Date: 31-03-2023 15:00:01

Number of reads: 1619732

Percentage reads mapped: 93.54

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.99
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7492 p.Phe64Ser missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7614 c.313C>T synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491298 c.516C>T synonymous_variant 0.15
fgd1 491305 p.Ala175Pro missense_variant 0.14
mshA 576197 p.Leu284Met missense_variant 0.14
mshA 576318 p.Arg324Pro missense_variant 0.12
mshA 576480 p.Pro378Arg missense_variant 0.17
ccsA 619717 c.-174G>C upstream_gene_variant 0.12
ccsA 619760 c.-131G>C upstream_gene_variant 0.13
ccsA 620119 p.Gly77Trp missense_variant 0.17
rpoC 764521 c.1152T>C synonymous_variant 0.11
rpoC 764551 c.1182G>C synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779202 c.-722G>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801225 c.417C>T synonymous_variant 0.15
Rv1258c 1407485 c.-145G>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.27
rrs 1471929 n.84C>G non_coding_transcript_exon_variant 0.33
rrs 1471930 n.85G>C non_coding_transcript_exon_variant 0.33
rrs 1471931 n.86G>T non_coding_transcript_exon_variant 0.33
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.33
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.3
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.5
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.33
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.33
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.38
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.43
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.43
rrs 1472168 n.323G>A non_coding_transcript_exon_variant 0.33
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.33
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 1.0
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 1.0
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.33
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.38
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.33
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.18
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.33
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 0.36
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.18
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.36
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.36
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 0.36
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.33
rrs 1472660 n.815T>A non_coding_transcript_exon_variant 0.27
rrs 1472666 n.821G>T non_coding_transcript_exon_variant 0.18
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.44
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.43
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.22
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.5
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.5
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.14
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.29
rrs 1472780 n.935G>A non_coding_transcript_exon_variant 0.15
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.17
rrs 1472837 n.992C>T non_coding_transcript_exon_variant 0.4
rrs 1472998 n.1153C>T non_coding_transcript_exon_variant 0.29
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.29
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.29
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.25
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.22
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.25
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.25
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.25
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.25
rrl 1473700 n.43G>T non_coding_transcript_exon_variant 0.4
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.22
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 1.0
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 1.0
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 1.0
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 1.0
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 1.0
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 1.0
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 1.0
rrl 1474672 n.1015C>A non_coding_transcript_exon_variant 0.67
rrl 1474797 n.1140G>C non_coding_transcript_exon_variant 0.5
rrl 1475277 n.1620G>A non_coding_transcript_exon_variant 0.4
rrl 1475301 n.1644T>A non_coding_transcript_exon_variant 0.67
rrl 1475814 n.2157A>G non_coding_transcript_exon_variant 0.17
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.27
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.27
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.2
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.5
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.2
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.2
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.33
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.25
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.29
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.25
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.29
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.67
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.14
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.18
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.25
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.25
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.29
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.22
rrl 1476540 n.2883C>A non_coding_transcript_exon_variant 0.29
rrl 1476566 n.2909A>T non_coding_transcript_exon_variant 0.29
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.29
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.5
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.5
rrl 1476608 n.2951C>T non_coding_transcript_exon_variant 0.5
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.6
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.6
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.67
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.75
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.67
inhA 1674968 p.Asp256Gly missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918039 p.Ile34Leu missense_variant 0.12
ndh 2101668 p.Ala459Pro missense_variant 0.15
ndh 2102883 c.160C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289903 c.-662C>A upstream_gene_variant 0.15
eis 2714871 c.462G>T synonymous_variant 0.19
eis 2714950 p.Arg128Leu missense_variant 0.2
eis 2714954 p.Gly127Ser missense_variant 0.27
pepQ 2860053 c.366G>A synonymous_variant 0.2
pepQ 2860082 p.Ala113Ser missense_variant 0.15
Rv2752c 3065603 p.Asp197His missense_variant 0.12
Rv2752c 3066299 c.-109delG upstream_gene_variant 0.12
thyX 3067209 p.Leu246Ser missense_variant 0.15
thyX 3067952 c.-7G>A upstream_gene_variant 0.2
thyA 3074427 c.45T>C synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339371 p.Pro85Leu missense_variant 0.15
fbiD 3339669 c.552C>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641249 p.Ala236Gly missense_variant 0.12
fbiA 3641257 p.Pro239Ala missense_variant 0.12
clpC1 4038201 p.Ala835Asp missense_variant 0.18
clpC1 4040057 c.648C>T synonymous_variant 0.18
clpC1 4040250 p.Glu152Gly missense_variant 0.13
embC 4242429 p.Ala856Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243714 p.Thr161Ser missense_variant 0.17
embA 4246461 p.Gly1077Cys missense_variant 0.15
embA 4246489 p.Arg1086Gln missense_variant 0.15
embA 4246498 p.Pro1089Gln missense_variant 0.18
embB 4246980 p.Gly156Asp missense_variant 0.17
embB 4247037 p.Gly175Asp missense_variant 0.25
embB 4248315 p.Ala601Asp missense_variant 0.16
embB 4249268 p.Asp919His missense_variant 0.13
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4326923 p.Gly184Asp missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0