TB-Profiler result

Run: SRR7645808
Summary

Run ID: SRR7645808

Sample name:

Date: 04-04-2023 19:52:52

Number of reads: 2570302

Percentage reads mapped: 36.78

Strain: lineage4.8;lineage4.2.1

Drug-resistance: HR-TB

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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 0.64
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.36
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.67
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 0.76 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.71 isoniazid
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 7585 p.Ser95Thr missense_variant 0.74
gyrA 9304 p.Gly668Asp missense_variant 0.59
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 0.42
fbiC 1304384 p.Val485Ala missense_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.14
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.15
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.16
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.33
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.34
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.35
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.63
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.68
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.83
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.82
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.82
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.81
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.83
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.83
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.23
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.19
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.34
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.55
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.6
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.78
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.77
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.77
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.72
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.69
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.38
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.24
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.24
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.21
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.16
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.15
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.11
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.26
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.19
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.1
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.11
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.18
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.25
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.36
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.4
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.41
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.44
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.44
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.43
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.42
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.39
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.4
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.4
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.4
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.42
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.15
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.14
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.15
rrl 1475688 n.2031G>C non_coding_transcript_exon_variant 0.15
rrl 1475692 n.2035G>A non_coding_transcript_exon_variant 0.16
rrl 1475695 n.2038G>A non_coding_transcript_exon_variant 0.15
rrl 1475699 n.2042C>A non_coding_transcript_exon_variant 0.15
rrl 1475704 n.2047C>T non_coding_transcript_exon_variant 0.17
rrl 1475707 n.2050T>C non_coding_transcript_exon_variant 0.17
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.15
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.16
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.31
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.32
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.32
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.38
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.4
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.41
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.37
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.13
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.1
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.75
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.79
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.85
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.85
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.86
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.85
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.87
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.87
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.88
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.82
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.77
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.69
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.65
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.63
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.62
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.6
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.59
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.59
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.59
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.6
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.61
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.59
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.49
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.47
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.47
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.46
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747536 c.63G>A synonymous_variant 0.73
thyA 3073806 c.666C>G synonymous_variant 0.14
ald 3086742 c.-78A>C upstream_gene_variant 0.61
ald 3086788 c.-32T>C upstream_gene_variant 0.58
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.6
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 0.69
ethA 4328376 c.-903G>C upstream_gene_variant 0.76
whiB6 4338595 c.-75delG upstream_gene_variant 1.0