TB-Profiler result

Run: ERR2513054
Summary

Run ID: ERR2513054

Sample name:

Date: 31-03-2023 19:26:01

Number of reads: 689107

Percentage reads mapped: 95.45

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.86 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
gyrA 6304 c.-998C>T upstream_gene_variant 0.15
gyrA 6728 c.-574C>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491644 p.Ser288Pro missense_variant 0.11
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoB 762895 p.Leu1030Pro missense_variant 0.14
rpoB 762940 c.3135delG frameshift_variant 0.17
rpoC 764548 c.1179G>T synonymous_variant 0.15
rpoC 764549 p.Pro394Val missense_variant 0.15
rpoC 764560 c.1191T>C synonymous_variant 0.15
rpoC 764566 c.1197C>G synonymous_variant 0.15
rpoC 764572 c.1203G>C synonymous_variant 0.14
rpoC 764575 c.1206T>G synonymous_variant 0.17
rpoC 764581 c.1212T>C synonymous_variant 0.17
rpoC 764582 p.Leu405Met missense_variant 0.17
rpoC 764605 c.1236G>C synonymous_variant 0.22
rpoC 764611 c.1242G>C synonymous_variant 0.22
rpoC 764620 c.1251G>C synonymous_variant 0.22
rpoC 764623 c.1254C>G synonymous_variant 0.22
rpoC 764632 c.1263T>C synonymous_variant 0.22
rpoC 764635 c.1266C>G synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776402 c.2079C>G synonymous_variant 1.0
mmpL5 777118 p.Asp455Asn missense_variant 0.12
mmpL5 777119 p.His454Gln missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.2
mmpL5 777128 c.1353A>G synonymous_variant 0.13
mmpL5 777140 c.1341G>C synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801075 c.267G>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.67
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.33
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.33
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.25
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.25
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.2
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.2
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.4
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.4
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.44
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.4
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.4
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.45
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.57
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.5
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.5
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.4
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.67
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.67
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.8
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.83
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.83
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.83
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.83
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.75
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.5
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.4
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 1.0
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.38
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.71
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.86
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.75
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.25
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.62
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.62
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.75
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.86
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.86
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.86
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.86
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.43
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.86
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.8
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.67
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.67
rrl 1475875 n.2219delA non_coding_transcript_exon_variant 0.4
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.18
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102401 c.642T>C synonymous_variant 0.15
ndh 2102407 c.636T>C synonymous_variant 0.15
katG 2155902 c.210C>T synonymous_variant 0.13
PPE35 2169056 c.1557A>G synonymous_variant 0.12
Rv1979c 2222499 c.666G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518857 p.Ile248Asn missense_variant 0.11
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448313 c.-191G>T upstream_gene_variant 0.25
fprA 3473988 c.-19A>G upstream_gene_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474996 c.990C>T synonymous_variant 0.13
alr 3841153 p.Gly90Ser missense_variant 0.12
clpC1 4039558 p.Ala383Thr missense_variant 0.14
clpC1 4039691 c.1014G>C synonymous_variant 0.13
clpC1 4039829 p.Leu292Phe missense_variant 0.1
embC 4240648 c.786C>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244785 p.Arg518Gln missense_variant 0.12
aftB 4268312 c.525G>A synonymous_variant 0.17
ethR 4327948 p.Val134Phe missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0