TB-Profiler result

Run: SRR6045110
Summary

Run ID: SRR6045110

Sample name:

Date: 04-04-2023 11:53:03

Number of reads: 1789645

Percentage reads mapped: 81.22

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 0.88 streptomycin
gid 4408100 c.102delG frameshift_variant 1.0 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8056 p.Arg252Leu missense_variant 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.23
rpoB 759746 c.-61C>T upstream_gene_variant 0.98
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile 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 1472106 n.261G>A non_coding_transcript_exon_variant 0.14
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.17
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.21
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.3
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.26
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.25
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.25
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.41
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.55
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.55
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.56
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.57
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.6
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.53
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.59
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.53
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.72
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.77
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.84
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.84
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.83
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.79
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.91
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 0.93
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.92
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.86
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.86
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.77
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.77
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.38
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.8
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.79
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.88
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.73
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.85
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.85
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.84
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.84
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.84
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.81
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.8
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.38
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.14
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.14
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.15
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.25
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.38
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.38
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.38
rrl 1474029 n.372G>T non_coding_transcript_exon_variant 0.33
rrl 1474208 n.551C>T non_coding_transcript_exon_variant 0.29
rrl 1474213 n.556G>A non_coding_transcript_exon_variant 0.29
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.57
rrl 1474228 n.571T>A non_coding_transcript_exon_variant 0.4
rrl 1474249 n.592G>A non_coding_transcript_exon_variant 0.5
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.67
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.5
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.67
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.67
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 1.0
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 1.0
rrl 1475552 n.1895G>C non_coding_transcript_exon_variant 1.0
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 1.0
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.5
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.5
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.5
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 1.0
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.67
rrl 1475760 n.2103C>A non_coding_transcript_exon_variant 0.5
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.71
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.78
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.7
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.8
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.8
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.8
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.67
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.5
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 1.0
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 1.0
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.67
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.67
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.67
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.5
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.5
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.33
rrl 1476090 n.2433C>A non_coding_transcript_exon_variant 0.29
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.75
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.6
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.6
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.74
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.77
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.74
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.78
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.68
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.6
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.6
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.6
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.57
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.52
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.45
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.48
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.48
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.52
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.56
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.66
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.7
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.79
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.83
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.79
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.8
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.8
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.85
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.88
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.11
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.85
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.55
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.18
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.12
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.13
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.19
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726012 c.-181T>C upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0