TB-Profiler result

Run: ERR4815528
Summary

Run ID: ERR4815528

Sample name:

Date: 01-04-2023 13:54:54

Number of reads: 385727

Percentage reads mapped: 75.06

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 0.71 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 6105 p.Ile289Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576390 p.Val348Ala missense_variant 0.25
rpoC 763655 p.Glu96Arg missense_variant 0.13
rpoC 763660 c.291T>G synonymous_variant 0.13
rpoC 763672 c.303C>G synonymous_variant 0.12
rpoC 763696 c.327T>C synonymous_variant 0.12
rpoC 763708 c.339G>C synonymous_variant 0.12
rpoC 763717 c.348T>C synonymous_variant 0.12
rpoC 764491 c.1122G>T synonymous_variant 0.17
rpoC 764497 c.1128A>G synonymous_variant 0.14
rpoC 764503 c.1134G>T synonymous_variant 0.17
rpoC 764509 c.1140G>C synonymous_variant 0.18
rpoC 764512 c.1143G>C synonymous_variant 0.17
rpoC 764521 c.1152T>C synonymous_variant 0.17
rpoC 764524 c.1155C>T synonymous_variant 0.17
rpoC 764530 c.1161C>T synonymous_variant 0.18
rpoC 764536 c.1167G>C synonymous_variant 0.17
rpoC 764543 p.Thr392Ala missense_variant 0.17
rpoC 764548 c.1179G>T synonymous_variant 0.18
rpoC 764566 c.1197C>G synonymous_variant 0.2
rpoC 764573 p.Leu402Ile missense_variant 0.2
rpoC 764578 c.1209C>G synonymous_variant 0.2
rpoC 764581 c.1212T>C synonymous_variant 0.18
rpoC 764582 p.Leu405Met missense_variant 0.17
rpoC 764602 c.1233C>T synonymous_variant 0.14
rpoC 764605 c.1236G>T synonymous_variant 0.14
rpoC 764611 c.1242G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781672 p.Tyr38Phe missense_variant 0.14
rplC 800986 p.Arg60Ser missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.8
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.7
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.78
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.83
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.83
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.83
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.79
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.79
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.84
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.8
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.63
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.84
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.88
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.88
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.9
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.86
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.8
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.8
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.78
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.64
rrs 1472685 n.840G>A non_coding_transcript_exon_variant 0.13
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.57
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.47
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.67
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.11
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.59
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.59
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.68
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.68
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.54
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.55
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.2
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.2
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.25
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.25
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.22
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.46
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.2
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.44
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.56
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.44
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.4
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.4
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.4
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.4
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.4
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.4
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.27
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.42
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.18
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.27
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.38
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.4
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.4
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.4
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.5
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.57
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.57
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.4
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.33
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.29
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.25
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.38
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 0.25
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.33
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.29
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.29
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.29
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.33
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.33
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.4
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.4
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.6
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.4
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.6
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.5
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.22
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.36
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169488 c.1125G>C synonymous_variant 0.15
PPE35 2169491 c.1122T>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.33
ahpC 2726341 p.Val50Gly missense_variant 0.43
alr 3840310 p.Arg371Trp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0