Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A0 F0 I1 R1
|
61 |
39.0 |
4165548 |
97.4% |
4057243 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,750,975 |
G→A |
intergenic (‑108/‑504) |
malP ← / → malT |
maltodextrin phosphorylase/HTH‑type transcriptional regulator MalT |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,750,975 | 0 | G | A | 100.0%
| 227.2
/ NA
| 65 | intergenic (‑108/‑504) | malP/malT | maltodextrin phosphorylase/HTH‑type transcriptional regulator MalT |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (37/28); total (37/28) |
TTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAC > NC_017635/3750929‑3751021
|
ttGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGCGTTGCGGAGAt > 2:1817172/1‑50 (MQ=255)
ttGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGAt > 1:2062032/1‑50 (MQ=255)
tGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGAt > 2:1290282/1‑49 (MQ=255)
gACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATg < 1:1076753/49‑1 (MQ=255)
gACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATg < 1:718039/49‑1 (MQ=255)
gACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATg < 1:644590/49‑1 (MQ=255)
aCCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGTGTTGCGGAGATGAg > 2:954424/1‑50 (MQ=255)
cTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCa < 1:1096196/50‑1 (MQ=255)
cTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCa < 1:55746/50‑1 (MQ=255)
cTTCCTAATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCa < 2:1403390/50‑1 (MQ=255)
tCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg > 2:789340/1‑50 (MQ=255)
tCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg > 1:1963131/1‑50 (MQ=255)
ccTCATCCTGCGGGGGATTAGGCAGGGAGGGGTTGCGGAGATGAGCAAg > 2:1435728/1‑49 (MQ=255)
ccTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCaa < 1:103292/48‑1 (MQ=255)
ccTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg > 2:266783/1‑49 (MQ=255)
ccTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg > 1:1863721/1‑49 (MQ=255)
cTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAgg > 2:245936/1‑49 (MQ=255)
cTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAgg < 2:1021393/49‑1 (MQ=255)
tCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGa > 1:329590/1‑49 (MQ=255)
aTCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAt > 1:327467/1‑50 (MQ=255)
aTCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAt < 1:1230419/50‑1 (MQ=255)
tCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAtg > 1:1470872/1‑50 (MQ=255)
tCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAtg > 2:703606/1‑50 (MQ=255)
ccTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAtgt > 2:1842650/1‑50 (MQ=255)
cGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAt < 1:1574655/49‑1 (MQ=255)
gggggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct < 2:1976423/50‑1 (MQ=255)
gggggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct > 2:1222908/1‑50 (MQ=255)
ggggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct > 2:633113/1‑49 (MQ=255)
gATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc < 1:770823/50‑1 (MQ=255)
gATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc > 2:1917405/1‑50 (MQ=255)
gATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc < 2:844784/50‑1 (MQ=255)
aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAcc < 2:705644/50‑1 (MQ=255)
aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAcc < 2:495961/50‑1 (MQ=255)
aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAcc < 1:1853913/50‑1 (MQ=255)
aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc > 1:1969135/1‑49 (MQ=255)
tAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCAc > 2:386198/1‑50 (MQ=255)
aGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCAc < 1:35771/49‑1 (MQ=255)
ggCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACtt < 1:724230/50‑1 (MQ=255)
ggCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACt < 2:2067047/49‑1 (MQ=255)
ggCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACt > 1:15373/1‑49 (MQ=255)
gCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACtt > 2:935253/1‑49 (MQ=255)
cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTaa < 1:1343091/50‑1 (MQ=255)
cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:130307/1‑49 (MQ=255)
cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:530466/1‑49 (MQ=255)
cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:1155322/1‑49 (MQ=255)
aGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTaaa < 2:570199/50‑1 (MQ=255)
aGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:570144/1‑48 (MQ=255)
aGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 2:1136270/1‑48 (MQ=255)
aGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:833906/1‑48 (MQ=255)
gggAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAg > 1:717226/1‑50 (MQ=255)
ggaggaGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGc < 1:1031226/50‑1 (MQ=255)
gaggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGc > 2:1135107/1‑49 (MQ=255)
aggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGc > 1:1984052/1‑48 (MQ=255)
aggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTa < 2:2081530/50‑1 (MQ=255)
aggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTa < 2:465715/50‑1 (MQ=255)
gagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGt > 2:538667/1‑50 (MQ=255)
gagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGt < 2:1477398/50‑1 (MQ=255)
gTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTg > 1:682405/1‑49 (MQ=255)
gTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGc < 1:1981861/50‑1 (MQ=255)
gCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCaaa > 1:2044149/1‑50 (MQ=255)
cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCaaa < 2:1480557/49‑1 (MQ=255)
cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAc > 1:617493/1‑50 (MQ=255)
cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAc > 2:78788/1‑50 (MQ=255)
cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAc < 1:290109/50‑1 (MQ=255)
cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAc > 2:866374/1‑50 (MQ=255)
|
TTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAC > NC_017635/3750929‑3751021
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACC > NC_017635/3750929‑3751022
|
TTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATG > M01420:85:000000000‑AC936:1:2114:17750:20565/1‑51 (MQ=60)
TGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATG < M01420:85:000000000‑AC936:1:2101:10406:17367/50‑1 (MQ=60)
TGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATG < M01420:85:000000000‑AC936:1:1110:25037:19951/50‑1 (MQ=60)
TGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATG < M01420:85:000000000‑AC936:1:1109:7940:19909/50‑1 (MQ=60)
CCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCA < M01420:85:000000000‑AC936:1:1101:25113:20932/51‑1 (MQ=60)
CCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCA < M01420:85:000000000‑AC936:1:2101:6242:23783/51‑1 (MQ=60)
TCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGG > M01420:85:000000000‑AC936:1:2113:19731:14533/1‑51 (MQ=60)
TCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAA < M01420:85:000000000‑AC936:1:1102:15895:12940/49‑1 (MQ=60)
CCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGG > M01420:85:000000000‑AC936:1:2112:23125:7726/1‑50 (MQ=60)
TCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAA > M01420:85:000000000‑AC936:1:1105:22127:13888/1‑50 (MQ=60)
CATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAT < M01420:85:000000000‑AC936:1:2103:4984:19478/51‑1 (MQ=60)
ATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATG > M01420:85:000000000‑AC936:1:1105:24177:13280/1‑51 (MQ=60)
TCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGT > M01420:85:000000000‑AC936:1:2106:8802:25594/1‑51 (MQ=60)
GCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAT < M01420:85:000000000‑AC936:1:2108:17628:11429/50‑1 (MQ=60)
GGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAC < M01420:85:000000000‑AC936:1:1111:28710:13877/51‑1 (MQ=60)
GATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACC < M01420:85:000000000‑AC936:1:2112:16978:3795/51‑1 (MQ=60)
ATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACC > M01420:85:000000000‑AC936:1:2113:20827:16239/1‑50 (MQ=60)
TAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCAC < M01420:85:000000000‑AC936:1:1101:19872:14956/50‑1 (MQ=60)
AGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTT < M01420:85:000000000‑AC936:1:1110:18323:22015/51‑1 (MQ=60)
GGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTT > M01420:85:000000000‑AC936:1:1101:17793:8669/1‑50 (MQ=60)
GCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA < M01420:85:000000000‑AC936:1:2105:25280:8584/51‑1 (MQ=60)
CAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:85:000000000‑AC936:1:1102:14902:21031/1‑50 (MQ=60)
CAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:85:000000000‑AC936:1:2102:7273:19096/1‑50 (MQ=60)
CAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:85:000000000‑AC936:1:1108:13265:7302/1‑50 (MQ=60)
AGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:85:000000000‑AC936:1:1112:9682:10782/1‑49 (MQ=60)
AGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:85:000000000‑AC936:1:1108:11351:19556/1‑49 (MQ=60)
GGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGC > M01420:85:000000000‑AC936:1:1110:25115:19691/1‑51 (MQ=60)
GGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGC < M01420:85:000000000‑AC936:1:1114:11210:27185/51‑1 (MQ=60)
AGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCT > M01420:85:000000000‑AC936:1:2113:5497:20597/1‑49 (MQ=60)
AGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGC < M01420:85:000000000‑AC936:1:2113:10286:19924/51‑1 (MQ=60)
GTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGC > M01420:85:000000000‑AC936:1:1110:27989:9170/1‑50 (MQ=60)
GCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAC < M01420:85:000000000‑AC936:1:1104:10286:24965/51‑1 (MQ=60)
GCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAC > M01420:85:000000000‑AC936:1:2114:27599:15454/1‑51 (MQ=60)
CGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACC > M01420:85:000000000‑AC936:1:1109:10513:11755/1‑51 (MQ=60)
CGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACC < M01420:85:000000000‑AC936:1:1105:11971:4276/51‑1 (MQ=60)
GGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACC > M01420:85:000000000‑AC936:1:1106:23617:16350/1‑50 (MQ=60)
|
TTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACC > NC_017635/3750929‑3751022
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
