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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,440,158 |
T→C |
41.8% |
K48K (AAA→AAG) |
ompC ← |
outer membrane porin protein C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,440,158 | 0 | T | C | 41.8%
| 16.3
/ 38.6
| 55 | K48K (AAA→AAG) | ompC | outer membrane porin protein C |
| Reads supporting (aligned to +/- strand): ref base T (29/3); new base C (2/21); total (31/24) |
| Fisher's exact test for biased strand distribution p-value = 5.09e-10 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01 |
TAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGT > minE/1440100‑1440225
|
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:983258/1‑66 (MQ=255)
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:2795273/1‑66 (MQ=255)
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:558065/1‑66 (MQ=255)
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:3155438/1‑66 (MQ=255)
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:540491/1‑66 (MQ=255)
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:3190400/1‑66 (MQ=255)
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:179851/1‑66 (MQ=255)
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:3287183/1‑66 (MQ=255)
tAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGCCGCCATCTACATCTTtgttgt > 1:2648753/1‑66 (MQ=255)
tAACCTGAGTTTCAACTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTtgttgt > 1:856935/1‑66 (MQ=255)
gAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTTGTTGTCAGAGAAAt < 1:948185/69‑1 (MQ=255)
gAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTTGTTGTCAGAGAAAt < 1:2407687/69‑1 (MQ=255)
gAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTTGTTGTCAGAGAAAt < 1:2393863/69‑1 (MQ=255)
ccAAGACGCATTTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:3270542/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATat < 1:552301/54‑2 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:3409691/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:2550684/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:2693041/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:1072774/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:547791/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:3112665/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:340463/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:244745/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:1194802/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:1416051/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:1566446/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:1856807/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:88895/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:1926416/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:2301143/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:2342291/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:2345868/54‑1 (MQ=255)
ccAAGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:587419/54‑1 (MQ=255)
aGACGCATGTAGGTCTGGTCGCCATCTACAGACTTGTCGTCAGAGAAATAg < 1:642649/51‑1 (MQ=255)
tAGGTCTGGTCGCCATCTACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTc > 1:3401855/1‑53 (MQ=255)
cTGGTCGCCATCTACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTaa > 1:3023826/1‑69 (MQ=255)
cTGGTCGCCATCTACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTaa > 1:3400980/1‑69 (MQ=255)
cTGGTCGCCATCTACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTaa > 1:2453165/1‑69 (MQ=255)
cTGGTCGCCATCTACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTa > 1:2306680/1‑68 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACt > 1:3296727/1‑40 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:821917/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:450527/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:2855934/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:3419055/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:3197362/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:3171722/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:2823002/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:260361/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:2359506/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:2231148/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:196538/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:1911918/1‑69 (MQ=255)
tACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:1410587/1‑69 (MQ=255)
tACATCCTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:3030294/1‑69 (MQ=255)
tACATCCTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTc > 1:1115928/1‑69 (MQ=255)
tttGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTttgt > 1:1971028/1‑68 (MQ=255)
|
TAACCTGAGTTTCACCTTTGAAGCCAAGACGCATGTAGGTCTGGTCGCCATCTACATCTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGT > minE/1440100‑1440225
|
| 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
