TB-Profiler result

Run: SRR10993936
Summary

Run ID: SRR10993936

Sample name:

Date: 02-04-2023 19:48:37

Number of reads: 1020159

Percentage reads mapped: 79.47

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
tlyA 1917940 c.2delT frameshift_variant 0.13 capreomycin
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 0.98
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 490751 c.-32T>G upstream_gene_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620768 p.Ala293Gly missense_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
Rv1258c 1407392 c.-52G>A upstream_gene_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.14
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.14
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.13
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.21
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.22
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.27
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.25
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.24
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.24
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.24
rrs 1472669 n.824_825insTAGA non_coding_transcript_exon_variant 0.26
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.25
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.25
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.24
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.24
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.25
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.25
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.24
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.24
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.24
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.24
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.3
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.23
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.17
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.1
rrs 1472861 n.1016G>C non_coding_transcript_exon_variant 0.1
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.18
rrs 1472967 n.1122G>T non_coding_transcript_exon_variant 0.12
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.11
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.13
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.13
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.13
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.13
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.2
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.19
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.2
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.19
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.2
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.18
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.14
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.14
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.13
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.13
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.16
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.19
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.21
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.21
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.21
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.2
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.21
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.23
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.23
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.17
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.17
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.15
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.16
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.16
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.13
rrl 1476022 n.2365A>G non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.15
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.41
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.39
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.39
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.4
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.38
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.39
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.37
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.38
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.38
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.39
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.4
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.4
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.44
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.51
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.54
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.52
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.51
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.53
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.52
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.53
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.54
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.52
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.45
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.37
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.34
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.34
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.34
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.34
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.34
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.34
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.34
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.34
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.33
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.31
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.28
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.27
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.26
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.16
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
katG 2156367 c.-256G>A upstream_gene_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
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 0.97
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 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
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 1.0
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