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 |
1,133,307 |
T→A |
51.0% |
P156P (CCA→CCT) |
ydiY ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,133,307 | 0 | T | A | 51.0%
| ‑3.9
/ 59.3
| 49 | P156P (CCA→CCT) | ydiY | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (18/6); new base A (9/16); total (27/22) |
| Fisher's exact test for biased strand distribution p-value = 9.60e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCCGGAGGCATAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGCCATTCAAAAACTGACGACCAT > minE/1133241‑1133362
|
cccGGAGGCATAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTgg > 1:2066319/1‑69 (MQ=255)
aTAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:1224260/1‑68 (MQ=255)
aTAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:29498/1‑68 (MQ=255)
aTAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:2196674/1‑68 (MQ=255)
aTAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:2107146/1‑68 (MQ=255)
tAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:1050531/1‑67 (MQ=255)
tAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:1239111/1‑67 (MQ=255)
tAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:1417625/1‑67 (MQ=255)
tAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:886095/1‑67 (MQ=255)
tAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:86204/1‑67 (MQ=255)
tAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAAtt > 1:222905/1‑67 (MQ=255)
gCCCAGCGGCTGGGTTTCTCTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCaaa > 1:1040855/1‑69 (MQ=255)
gCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAAtt > 1:2893748/1‑65 (MQ=255)
gCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCaaa > 1:3043715/1‑69 (MQ=255)
gCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCaaa > 1:2660972/1‑69 (MQ=255)
gCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCaaa > 1:2304343/1‑69 (MQ=255)
gCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCaaa > 1:637578/1‑69 (MQ=255)
gCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCaaa > 1:719299/1‑69 (MQ=255)
gCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCaaa > 1:729922/1‑69 (MQ=255)
gCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCaa > 1:3409404/1‑68 (MQ=255)
cTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACt < 1:3094716/69‑1 (MQ=255)
cTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACt < 1:124779/69‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGc < 1:1962125/69‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGc < 1:2826845/69‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAATTCAAAGCCGAAACTGTGTACCGGGc < 1:104007/69‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:3368258/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:3317818/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:3304121/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:3273388/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:3231964/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:939876/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:1755535/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:1765243/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:2431375/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:2241177/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:2073342/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:1814854/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:1907490/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:1861641/59‑1 (MQ=255)
tGGCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:1855939/59‑1 (MQ=255)
ggCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGcc < 1:2461208/69‑1 (MQ=255)
ggCATTGTCGGTATATTTGTCGTAACGCACACCAGGGCCGAATTCAAAGCGGAAACtg < 1:2452268/58‑1 (MQ=255)
tttGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGCCATTCAAAAACTgacg > 1:664826/1‑69 (MQ=255)
tttGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGCCATTCAAAAACTgacg > 1:771338/1‑69 (MQ=255)
tttGTCGTAACCCACACCTGGACCGAATTCAAAGCGGAAACTGTGAACCGGGCCATTCAAAAACTgacg > 1:2735237/1‑69 (MQ=255)
tGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGCCATTCAAAAACTgacgac > 1:625559/1‑69 (MQ=255)
tGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGCCATTCAAAAACTgacga > 1:3102491/1‑68 (MQ=255)
gTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGCCATTCAAAAACTGACGACCAt > 1:534818/1‑68 (MQ=255)
gTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGCCATTCAAAAACTGACGACCAt > 1:2493834/1‑68 (MQ=255)
|
CCCGGAGGCATAGCCCAGCGGCTGGGTTTCACTGGCATTGTCGGTATATTTGTCGTAACGCACACCTGGACCGAATTCAAAGCGGAAACTGTGTACCGGGCCATTCAAAAACTGACGACCAT > minE/1133241‑1133362
|
| 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
