TB-Profiler result

Run: SRR7851312
Summary

Run ID: SRR7851312

Sample name:

Date: 04-04-2023 20:22:49

Number of reads: 3252955

Percentage reads mapped: 87.49

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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.34 streptomycin
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 7475 c.174A>G synonymous_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7821 c.520C>T synonymous_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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575793 p.Asp149Gly missense_variant 1.0
rpoB 762197 c.2391C>G synonymous_variant 0.11
rpoB 762218 c.2412T>C synonymous_variant 0.12
rpoB 762233 c.2427G>C synonymous_variant 0.14
rpoB 762245 c.2439G>C synonymous_variant 0.14
rpoB 762254 c.2448T>C synonymous_variant 0.16
rpoB 762266 c.2460T>C synonymous_variant 0.16
rpoB 762284 c.2478G>C synonymous_variant 0.13
rpoC 762971 c.-399G>C upstream_gene_variant 0.1
rpoC 762989 c.-381G>C upstream_gene_variant 0.14
rpoC 762995 c.-375G>C upstream_gene_variant 0.14
rpoB 763005 p.Cys1067Gly missense_variant 0.11
rpoC 763013 c.-357C>A upstream_gene_variant 0.11
rpoC 763022 c.-348C>G upstream_gene_variant 0.13
rpoC 763028 c.-342T>C upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763052 c.-318G>T upstream_gene_variant 0.11
rpoC 763088 c.-282C>G upstream_gene_variant 0.12
rpoC 763094 c.-276G>C upstream_gene_variant 0.12
rpoC 763106 c.-264C>T upstream_gene_variant 0.13
rpoC 763115 c.-255T>C upstream_gene_variant 0.13
rpoB 763118 p.Glu1104Asp missense_variant 0.12
rpoB 763130 p.Glu1108Asp missense_variant 0.11
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
rpsL 781802 c.243G>C synonymous_variant 0.11
rpsL 781817 c.258G>C synonymous_variant 0.12
rpsL 781832 c.273T>G synonymous_variant 0.15
rpsL 781859 c.300T>C synonymous_variant 0.11
rpsL 781860 p.Ser101Ala missense_variant 0.11
rpsL 781871 c.312G>C synonymous_variant 0.1
rpsL 781880 c.321C>G synonymous_variant 0.11
rpsL 781884 p.Asn109Asp missense_variant 0.11
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.12
rrs 1471925 n.80T>G non_coding_transcript_exon_variant 0.19
rrs 1471929 n.84C>G non_coding_transcript_exon_variant 0.19
rrs 1471931 n.87_89delAGA non_coding_transcript_exon_variant 0.2
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.19
rrs 1472057 n.212C>T non_coding_transcript_exon_variant 0.18
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.19
rrs 1472062 n.217G>T non_coding_transcript_exon_variant 0.2
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.28
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.31
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.31
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.39
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.45
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.43
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.26
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.41
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.42
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.4
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.28
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.28
rrs 1472671 n.826G>A non_coding_transcript_exon_variant 0.22
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.22
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.23
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.29
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.13
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.22
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.39
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.38
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.44
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.42
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.21
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.35
rrl 1473677 n.20C>T non_coding_transcript_exon_variant 0.15
rrl 1473697 n.40C>G non_coding_transcript_exon_variant 0.18
rrl 1473698 n.41G>C non_coding_transcript_exon_variant 0.18
rrl 1473699 n.42A>T non_coding_transcript_exon_variant 0.18
rrl 1473718 n.61G>T non_coding_transcript_exon_variant 0.18
rrl 1473728 n.71A>T non_coding_transcript_exon_variant 0.15
rrl 1473743 n.86C>T non_coding_transcript_exon_variant 0.15
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.15
rrl 1473751 n.94C>A non_coding_transcript_exon_variant 0.15
rrl 1473752 n.95G>A non_coding_transcript_exon_variant 0.15
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.16
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.14
rrl 1474130 n.473C>T non_coding_transcript_exon_variant 0.2
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.24
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.3
rrl 1474182 n.525C>A non_coding_transcript_exon_variant 0.33
rrl 1474183 n.526T>G non_coding_transcript_exon_variant 0.34
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.34
rrl 1474185 n.529delA non_coding_transcript_exon_variant 0.34
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.37
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.14
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.11
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.11
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.12
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.12
rrl 1474487 n.830G>T non_coding_transcript_exon_variant 0.13
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.12
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.12
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.12
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.12
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.13
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.14
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.14
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.13
rrl 1474517 n.860C>G non_coding_transcript_exon_variant 0.28
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.36
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.17
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.17
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.18
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.18
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.18
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.22
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.31
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.27
rrl 1474798 n.1141C>G non_coding_transcript_exon_variant 0.28
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.31
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.27
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.27
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.26
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.28
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.3
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.29
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.16
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.14
rrl 1474904 n.1247G>T non_coding_transcript_exon_variant 0.12
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.12
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.14
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.13
rrl 1475525 n.1868G>A non_coding_transcript_exon_variant 0.15
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.15
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.15
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 0.15
rrl 1475539 n.1882A>G non_coding_transcript_exon_variant 0.15
rrl 1475542 n.1885A>G non_coding_transcript_exon_variant 0.15
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.16
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.16
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.16
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.24
rrl 1475769 n.2112_2113insC non_coding_transcript_exon_variant 0.25
rrl 1475879 n.2222T>C non_coding_transcript_exon_variant 0.29
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.28
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.28
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.28
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.37
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.37
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.38
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.42
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.44
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.43
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.32
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.32
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.23
rrl 1475989 n.2332T>C non_coding_transcript_exon_variant 0.23
rrl 1475990 n.2333G>A non_coding_transcript_exon_variant 0.23
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.24
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.13
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.18
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.31
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.31
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.31
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.24
rrl 1476215 n.2558_2559insTA non_coding_transcript_exon_variant 0.25
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.33
rrl 1476255 n.2598A>T non_coding_transcript_exon_variant 0.28
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.28
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.34
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.35
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.27
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.28
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.27
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.27
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.3
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.56
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.46
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.37
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.38
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.38
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.31
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.28
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.2
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.2
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
rpsA 1833422 c.-120G>T upstream_gene_variant 1.0
rpsA 1834501 c.960G>C synonymous_variant 0.11
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 p.Gly313Arg missense_variant 0.99
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
PPE35 2169320 p.Leu431Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.42
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170066 p.Ala183Thr missense_variant 0.17
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 2518654 c.540C>T synonymous_variant 1.0
thyX 3067786 p.Thr54Ala missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.3
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
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
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 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