TB-Profiler result

Run: SRR10993944
Summary

Run ID: SRR10993944

Sample name:

Date: 02-04-2023 19:48:52

Number of reads: 1143555

Percentage reads mapped: 82.13

Strain: La1.6

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
La1.6 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 7042 c.-260C>T upstream_gene_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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.14
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.1
rrl 1473539 n.-119C>G upstream_gene_variant 1.0
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.13
rrl 1476196 n.2539C>G non_coding_transcript_exon_variant 0.13
rrl 1476197 n.2540T>C non_coding_transcript_exon_variant 0.13
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.13
rrl 1476209 n.2552A>G non_coding_transcript_exon_variant 0.13
rrl 1476210 n.2553G>C non_coding_transcript_exon_variant 0.13
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.13
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.13
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.14
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.13
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.13
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.2
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.2
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.22
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.29
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.28
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.28
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.28
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.28
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.28
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.27
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.27
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.28
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.3
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.32
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.32
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.32
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.31
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.34
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.34
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.32
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.3
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.26
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.26
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.24
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
rrl 1476513 n.2856G>A non_coding_transcript_exon_variant 0.13
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.12
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.12
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.12
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.12
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.14
rrl 1476544 n.2887T>C non_coding_transcript_exon_variant 0.11
rrl 1476563 n.2907_2908insAGTG non_coding_transcript_exon_variant 0.12
rrl 1476572 n.2915G>C non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
rrl 1476592 n.2935G>A non_coding_transcript_exon_variant 0.12
rrl 1476605 n.2948C>T non_coding_transcript_exon_variant 0.12
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.12
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.12
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.12
rrl 1476624 n.2967T>C non_coding_transcript_exon_variant 0.12
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.12
rrl 1476637 n.2980C>A non_coding_transcript_exon_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223062 p.Thr35Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223320 c.-156T>C upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
folC 2746245 p.Ala452Thr missense_variant 1.0
ribD 2987615 c.777A>G stop_lost&splice_region_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_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 3474957 c.951G>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3611987 p.Leu377Pro missense_variant 1.0
rpoA 3878534 c.-27C>T upstream_gene_variant 0.17
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040033 c.672G>A synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
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
embB 4246551 p.Asn13Ser missense_variant 0.94
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247791 c.1278C>T synonymous_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