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 |
|
A2 F3 I0 R2
|
232 |
76.3 |
4135488 |
90.9% |
3759158 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
813,910 |
A→G |
17.9% |
C60C (TGT→TGC) |
prsA ← |
phosphoribosylpyrophosphate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 813,910 | 0 | A | G | 17.9%
| 152.4
/ 28.2
| 67 | C60C (TGT→TGC) | prsA | phosphoribosylpyrophosphate synthase |
| Reads supporting (aligned to +/- strand): ref base A (29/26); new base G (5/7); total (34/33) |
| Fisher's exact test for biased strand distribution p-value = 5.39e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01 |
GACCTGCGGAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATCACCACCGCGTACATTTTCATTAATTTGTACGCTG > minE/813840‑813970
|
gACCTGCGGAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGca > 1:3242315/1‑71 (MQ=255)
aCCTGCGGAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGca > 1:4110836/1‑70 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:3642383/1‑71 (MQ=255)
aGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTg < 1:2601905/67‑1 (MQ=255)
aGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTg < 1:3185056/67‑1 (MQ=255)
aGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTg < 1:1708862/67‑1 (MQ=255)
gCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTg < 1:1636124/71‑1 (MQ=255)
gCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGt > 1:1308082/1‑53 (MQ=255)
gCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaaaa > 1:2536673/1‑70 (MQ=255)
cATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAata > 1:1409403/1‑71 (MQ=255)
cATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAG‑AGGGGCGCAAGTGGACTGGATGATGAAAatat > 1:2694854/1‑71 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACaa > 1:5221/1‑46 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACaa > 1:3037445/1‑46 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACaa > 1:698361/1‑46 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACaa > 1:783340/1‑46 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACaa > 1:1500514/1‑46 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACaa > 1:1467460/1‑46 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACaa > 1:3512542/1‑46 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:143186/1‑51 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGga > 1:8869/1‑56 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGga > 1:2584704/1‑56 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATcac < 1:830583/71‑1 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATcac > 1:183838/1‑71 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATcac > 1:145870/1‑71 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATcac < 1:598629/71‑1 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATcac > 1:413930/1‑71 (MQ=255)
aaCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATcac < 1:961755/71‑1 (MQ=255)
aCCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTgg < 1:3259146/54‑1 (MQ=255)
aTAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:3625800/1‑47 (MQ=255)
aTAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:1127271/1‑47 (MQ=255)
aTAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:2562398/1‑47 (MQ=255)
aTAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:732955/1‑47 (MQ=255)
aTAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:80591/1‑47 (MQ=255)
aTAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:2108356/1‑47 (MQ=255)
aTAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGa > 1:934751/1‑47 (MQ=255)
aTAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATcaccac > 1:1107230/1‑70 (MQ=255)
tAACGTCTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAata < 1:3196584/62‑1 (MQ=255)
tAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGa < 1:525224/46‑1 (MQ=255)
tAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGa < 1:561021/46‑1 (MQ=255)
tAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGa < 1:1409601/46‑1 (MQ=255)
tAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAata < 1:4103436/62‑1 (MQ=255)
aCGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAATATCACCACcgcg > 1:2893400/1‑71 (MQ=255)
aCGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAATATCACCACcgc > 1:2457348/1‑70 (MQ=255)
aCGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAatat > 1:3149537/1‑61 (MQ=255)
aCGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAatat > 1:2548450/1‑61 (MQ=255)
aCGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATCACCACcgcg > 1:2408642/1‑71 (MQ=255)
cGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATcacc < 1:1163427/64‑1 (MQ=255)
tAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaa < 1:3937579/51‑1 (MQ=255)
tAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaa < 1:2945106/51‑1 (MQ=255)
tAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaa < 1:795273/51‑1 (MQ=255)
aTTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATCACCACCGCGTACAt < 1:3365405/69‑1 (MQ=255)
aTTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATCACCACCGCGTACAt < 1:3039575/69‑1 (MQ=255)
ttCCATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAATATCACCACCGCGTACAtttt < 1:1253497/71‑1 (MQ=255)
ttCCATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAATATCACCACCGCGTACAtttt < 1:878994/71‑1 (MQ=255)
ttCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaaa < 1:1434031/49‑1 (MQ=255)
ttCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaaa < 1:2147547/49‑1 (MQ=255)
ttCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaaa < 1:3880983/49‑1 (MQ=255)
ttCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATCACCACCGCGTACAtttt < 1:2195652/71‑1 (MQ=255)
ccATCAGGTTGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAATATCACCACCGCGTACATTTTc > 1:2298348/1‑70 (MQ=255)
ccATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGga > 1:3990325/1‑39 (MQ=255)
ccATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATCACCACCGCGTACATTTTCa > 1:862402/1‑71 (MQ=255)
tGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAata < 1:780522/41‑1 (MQ=255)
gTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaa < 1:2400505/36‑1 (MQ=255)
gTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaa < 1:2802300/36‑1 (MQ=255)
gTCGTTAGTAGGGGCACAAGTGGACTGGATGATGaa < 1:3390821/36‑1 (MQ=255)
cGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAata < 1:482536/38‑1 (MQ=255)
ttAGTAGGGGCACAAGTGGACTGGATGATGAAAATATCACCACCGCGTACATTTTCATTAATTTGTACGCt < 1:972097/71‑1 (MQ=255)
agtagGGGCGCAAGTGGACTGGATGATGAAAATATCACCACCGCGTACATTTTCATTAATTTGTACGCTg < 1:1898771/70‑1 (MQ=255)
agtagGGGCGCAAGTGGACAGGATGATGAAAATATCACCACCGCGTACATTTTCATTAATTTGTACGCTg < 1:801380/70‑1 (MQ=255)
|
GACCTGCGGAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAATATCACCACCGCGTACATTTTCATTAATTTGTACGCTG > minE/813840‑813970
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
