TB-Profiler result

Run: SRR1049743
Summary

Run ID: SRR1049743

Sample name:

Date: 02-04-2023 18:23:07

Number of reads: 1999823

Percentage reads mapped: 40.61

Strain: lineage4.6.1

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
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 9304 p.Gly668Asp missense_variant 1.0
rpoC 762899 c.-471G>C upstream_gene_variant 0.21
rpoC 762917 c.-453C>G upstream_gene_variant 0.2
rpoC 762920 c.-450C>T upstream_gene_variant 0.22
rpoC 762923 c.-447C>G upstream_gene_variant 0.2
rpoB 762925 p.Thr1040Ile missense_variant 0.21
rpoB 762939 p.Met1045Leu missense_variant 0.22
rpoB 762942 p.Ile1046Val missense_variant 0.22
rpoC 762962 c.-408C>T upstream_gene_variant 0.21
rpoC 762989 c.-381G>C upstream_gene_variant 0.12
rpoC 764557 p.Asn396Lys missense_variant 0.1
rpoC 764566 c.1197C>G synonymous_variant 0.29
rpoC 764575 c.1206T>G synonymous_variant 0.31
rpoC 764581 c.1212T>C synonymous_variant 0.34
rpoC 764582 p.Leu405Met missense_variant 0.31
rpoC 764587 c.1218C>G synonymous_variant 0.36
rpoC 764605 c.1236G>C synonymous_variant 0.4
rpoC 764611 c.1242G>T synonymous_variant 0.44
rpoC 764632 c.1263T>C synonymous_variant 0.35
rpoC 764641 c.1272C>T synonymous_variant 0.39
rpoC 764650 c.1281G>T synonymous_variant 0.36
rpoC 764663 p.Val432Thr missense_variant 0.16
rpoC 764668 c.1299C>T synonymous_variant 0.15
rpoC 764672 p.Gln435Glu missense_variant 0.15
rpoC 764677 c.1308C>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.26
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.4
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.42
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.39
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.38
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.38
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.31
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.26
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.24
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.24
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.19
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.13
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.13
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.13
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.14
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.14
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.15
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.15
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.29
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.28
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.28
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.49
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.51
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.49
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.46
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.35
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.21
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.18
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.1
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.19
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.19
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.22
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.22
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.16
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.35
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.46
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.46
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.46
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.53
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.53
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.62
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.63
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.75
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.76
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.73
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.68
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.62
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.61
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.57
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.49
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.37
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.27
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918596 c.657C>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0