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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,040,951 |
T→A |
38.3% |
*120K (TAA→AAA) |
yqiH → |
predicted periplasmic pilin chaperone |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,040,951 | 0 | T | A | 38.3%
| 28.5
/ 51.2
| 47 | *120K (TAA→AAA) | yqiH | predicted periplasmic pilin chaperone |
| Reads supporting (aligned to +/- strand): ref base T (14/15); new base A (13/5); total (27/20) |
| Fisher's exact test for biased strand distribution p-value = 1.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.74e-01 |
AAAAATTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCAA > minE/2040884‑2041017
|
aaaaaTTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCaaaa > 1:1455985/1‑71 (MQ=255)
aaaaTTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCaaaa > 1:2107142/1‑70 (MQ=255)
aaTTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCaaaa > 1:832095/1‑68 (MQ=255)
gCTCAACTTCCTAAAGACAGAGAACCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATa > 1:2369779/1‑70 (MQ=255)
gCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATa > 1:2219614/1‑70 (MQ=255)
cTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaa < 1:1359614/70‑1 (MQ=255)
cAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaa > 1:3700664/1‑70 (MQ=255)
aaCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaa > 1:3910544/1‑70 (MQ=255)
aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATaaaaaa > 1:3836165/1‑70 (MQ=255)
aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaaa < 1:570795/71‑1 (MQ=255)
aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaa > 1:3658399/1‑70 (MQ=255)
aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaa > 1:1844045/1‑68 (MQ=255)
cTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATaaaaaaaa > 1:3533897/1‑71 (MQ=255)
ccTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAAtgt > 1:3512989/1‑71 (MQ=255)
ccTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAAtg < 1:923492/70‑1 (MQ=255)
aGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTaa < 1:567901/49‑1 (MQ=255)
aGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTaa < 1:1976690/49‑1 (MQ=255)
gagaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGt < 1:561721/70‑1 (MQ=255)
gagaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGt > 1:3684748/1‑70 (MQ=255)
agaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCa > 1:2330655/1‑66 (MQ=255)
gaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCAc < 1:1825604/71‑1 (MQ=255)
aaaCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTaa < 1:2865738/41‑1 (MQ=255)
cGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATg < 1:3361794/71‑1 (MQ=255)
gCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATg > 1:2088619/1‑70 (MQ=255)
gCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATg > 1:1078297/1‑70 (MQ=255)
ctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTa > 1:3289688/1‑62 (MQ=255)
ctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTAt > 1:2888146/1‑63 (MQ=255)
ctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCAc < 1:1061969/70‑1 (MQ=255)
ctATTTTAACGTGCGAGAAATACCGCCCACAACAGATAAAAAAAATGTGATg > 1:610022/1‑52 (MQ=255)
ctATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACg > 1:981902/1‑71 (MQ=255)
ttttAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGc < 1:3140684/69‑1 (MQ=255)
ttAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTAt > 1:3927522/1‑58 (MQ=255)
aaCGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGa < 1:3888023/70‑1 (MQ=255)
tGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATg < 1:1253610/53‑1 (MQ=255)
cGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgca > 1:208727/1‑53 (MQ=255)
gagaAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTc < 1:2778175/71‑1 (MQ=255)
gagaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCaa > 1:2287940/1‑41 (MQ=255)
gaAATACCGCCCTAAACAGATAAAAAAAATGTGATg > 1:3459798/1‑36 (MQ=255)
gaAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCt > 1:2046976/1‑70 (MQ=255)
gaAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTg < 1:3093866/71‑1 (MQ=255)
gaAATACCGCCCAAAACAGATAAAAAAAATGTGAt < 1:3771182/35‑1 (MQ=255)
aaaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc < 1:2638720/43‑1 (MQ=255)
aaaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc < 1:2167216/43‑1 (MQ=255)
aaaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTgg > 1:698145/1‑71 (MQ=255)
aaaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGAAGCACGCATTGAAACTATTCTg > 1:532268/1‑70 (MQ=255)
aaaTACCGCCCAAAACAGATAAAAAAAATGTGATGCaa > 1:20609/1‑38 (MQ=255)
aaaTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTgg > 1:3825791/1‑71 (MQ=255)
aaaTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTgg > 1:3691071/1‑71 (MQ=255)
aTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTggcg < 1:234308/71‑1 (MQ=255)
gCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCaa < 1:2581458/71‑1 (MQ=255)
tAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTgg > 1:1543973/1‑60 (MQ=255)
|
AAAAATTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCAA > minE/2040884‑2041017
|
| 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
