TB-Profiler result

Run: SRR5067459

Summary

Run ID: SRR5067459

Sample name:

Date: 04-04-2023 08:27:43

Number of reads: 2204939

Percentage reads mapped: 81.4

Strain: lineage4.2

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 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407967 p.Leu79Ser missense_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 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
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 1472616 n.771G>A non_coding_transcript_exon_variant 0.19
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.29
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.27
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.26
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.26
rrs 1472669 n.824_825insTAGA non_coding_transcript_exon_variant 0.29
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.28
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.28
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.29
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.28
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.28
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.27
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.28
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.28
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.28
rrl 1474758 n.1101G>A non_coding_transcript_exon_variant 0.13
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.26
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.26
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.27
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.27
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.27
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.27
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.27
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.28
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.25
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.25
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.25
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.25
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.27
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.27
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.27
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.26
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.22
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.2
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.18
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.13
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.1
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.14
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.15
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.16
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.16
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.16
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.16
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.15
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.15
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.15
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.15
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.15
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.15
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.15
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.23
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.21
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.38
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.41
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.36
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.31
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.31
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.3
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.28
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.28
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.29
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.29
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.32
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.31
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.35
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.41
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.46
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.46
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.43
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.43
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.35
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.38
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.39
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.46
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.22
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.19
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.19
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.19
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.19
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.19
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.2
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.19
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.19
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.2
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.19
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.18
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.17
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.16
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066276 c.-85G>A upstream_gene_variant 0.99
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.99
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474394 p.Gly130Ser missense_variant 1.0
Rv3236c 3612469 c.648A>G synonymous_variant 1.0
rpoA 3878565 c.-58G>A upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0