TB-Profiler result

Run: SRR7535081
Summary

Run ID: SRR7535081

Sample name:

Date: 04-04-2023 19:44:16

Number of reads: 364635

Percentage reads mapped: 6.07

Strain: lineage4.6.1.1

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.1 Euro-American T2-Uganda RD724 0.97
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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8375 c.1074G>C synonymous_variant 1.0
gyrA 9144 p.Arg615Cys missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760223 c.417T>C synonymous_variant 0.25
rpoB 760306 p.Arg167Pro missense_variant 0.2
rpoC 762894 c.-476C>T upstream_gene_variant 0.56
rpoB 762911 p.Ile1035Met missense_variant 0.74
rpoC 762923 c.-447C>G upstream_gene_variant 0.67
rpoC 762929 c.-441G>T upstream_gene_variant 0.7
rpoC 762932 c.-438G>T upstream_gene_variant 0.7
rpoB 762939 p.Met1045Leu missense_variant 0.7
rpoB 762942 p.Ile1046Val missense_variant 0.67
rpoC 762947 c.-423C>G upstream_gene_variant 0.67
rpoC 762962 c.-408C>T upstream_gene_variant 0.62
rpoC 762989 c.-381G>T upstream_gene_variant 0.67
rpoC 762998 c.-372G>A upstream_gene_variant 0.58
rpoB 763002 c.3197dupA frameshift_variant 0.29
rpoC 764854 c.1485G>C synonymous_variant 0.45
rpoC 764858 p.Leu497Met missense_variant 0.45
rpoC 764869 c.1500C>T synonymous_variant 0.5
rpoC 764872 c.1503A>G synonymous_variant 0.5
rpoC 764875 c.1506C>T synonymous_variant 0.5
rpoC 764878 c.1509C>G synonymous_variant 0.5
rpoC 764887 c.1518G>T synonymous_variant 0.42
rpoC 764893 c.1524T>C synonymous_variant 0.38
rpoC 764905 c.1536C>T synonymous_variant 0.57
rpoC 764911 c.1542A>C synonymous_variant 0.53
rpoC 764914 p.Met515Ile missense_variant 0.53
rpoC 764918 p.Val517Ile missense_variant 0.57
rpoC 764939 c.1570C>T synonymous_variant 0.33
rpoC 764947 c.1578G>C synonymous_variant 0.25
rpoC 764948 c.1579_1581delTTGinsCTC synonymous_variant 0.25
rpoC 764953 c.1584G>T synonymous_variant 0.25
rpoC 764956 c.1587T>C synonymous_variant 0.25
rpoC 764958 p.Glu530Ala missense_variant 0.25
rpoC 764962 c.1593G>C synonymous_variant 0.25
rpoC 764968 c.1599T>C synonymous_variant 0.25
rpoC 766061 p.Val898Leu missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302837 c.-94G>A upstream_gene_variant 0.18
embR 1417372 c.-25C>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.33
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.85
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.94
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.94
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.97
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.97
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.97
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 1.0
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0
rrs 1472278 n.433C>T non_coding_transcript_exon_variant 0.75
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.67
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.96
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.96
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.84
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.79
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.79
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.79
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.79
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.83
rrs 1472824 n.979T>C non_coding_transcript_exon_variant 0.6
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.67
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.67
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.67
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.67
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.33
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.45
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.57
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.57
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.62
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.62
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.82
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.82
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.82
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.9
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.75
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.67
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.67
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.87
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.87
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.86
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.86
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.86
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.86
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.91
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.95
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.95
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.95
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.94
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.94
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.92
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.91
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.82
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.82
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.81
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.81
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.8
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.8
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.8
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.75
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.38
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065373 c.819A>G synonymous_variant 0.2
thyX 3067763 c.183C>A synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
panD 4043882 p.Pro134Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
ethA 4328389 c.-916C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0