TB-Profiler result

Run: SRR5486086
Summary

Run ID: SRR5486086

Sample name:

Date: 04-04-2023 10:28:06

Number of reads: 655800

Percentage reads mapped: 92.02

Strain: La1.2

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
La1 M.bovis None None 1.0
La1.2 M.bovis None 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
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576782 p.Gly479Arg missense_variant 0.13
rpoB 759620 c.-187A>C upstream_gene_variant 0.3
rpoB 760369 p.Ser188Tyr missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763930 p.Glu187Asp missense_variant 0.14
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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.33
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.33
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.33
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.33
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.33
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.6
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.6
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.6
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.43
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.71
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.6
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.6
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.43
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.43
rrs 1473181 n.1336C>T non_coding_transcript_exon_variant 0.29
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.43
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.3
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.33
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.33
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 1.0
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 1.0
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 1.0
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 1.0
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.29
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.29
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.29
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.67
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.67
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.67
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.67
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.67
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.67
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.67
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.67
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.67
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.67
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.67
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.9
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.9
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.82
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.75
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.75
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.69
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.69
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.69
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.69
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.69
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.69
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.69
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.69
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.69
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.69
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.71
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.71
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.71
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.69
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.69
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.64
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.64
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.64
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.64
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.56
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.62
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.5
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.5
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.5
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.5
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.5
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.5
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.4
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.4
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.4
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.4
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.4
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.67
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.67
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.67
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.67
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.5
rpsA 1833374 c.-168C>T upstream_gene_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 p.Gly313Arg missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519143 c.1029G>C synonymous_variant 0.1
pepQ 2860244 c.175C>A synonymous_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Ala missense_variant 0.1
ald 3087084 c.266delA frameshift_variant 1.0
fbiD 3339154 p.Ile13Leu missense_variant 1.0
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240801 c.939C>T synonymous_variant 0.12
embC 4240803 p.Tyr314Phe missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244818 p.Phe529Ser missense_variant 0.12
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0