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 |
1,337,480 |
A→G |
43.3% |
S5S (AGT→AGC) |
wcaF ← |
predicted acyl transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,337,480 | 0 | A | G | 43.3%
| 20.8
/ 65.4
| 57 | S5S (AGT→AGC) | wcaF | predicted acyl transferase |
| Reads supporting (aligned to +/- strand): ref base A (16/16); new base G (12/12); total (29/28) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTA > minE/1337418‑1337546
|
gCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATc > 1:2205602/1‑71 (MQ=255)
ccaTAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCa > 1:1093028/1‑71 (MQ=255)
aTAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCAtt > 1:3313574/1‑71 (MQ=255)
ttGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCAtt > 1:3074695/1‑67 (MQ=255)
cACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAAt < 1:2337958/56‑1 (MQ=255)
aCTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAAACTTGCATTGGTTTTcc < 1:2002535/71‑1 (MQ=255)
tttAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCtt > 1:89991/1‑56 (MQ=255)
tAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATc < 1:778262/52‑1 (MQ=255)
tAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTta > 1:1419153/1‑70 (MQ=255)
aaTAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTtat < 1:754543/70‑1 (MQ=255)
tAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTc > 1:2017027/1‑63 (MQ=255)
tAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATAtt < 1:2862722/71‑1 (MQ=255)
gCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATAtt > 1:2381423/1‑69 (MQ=255)
gCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATAtt > 1:3503435/1‑69 (MQ=255)
ccGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCa < 1:887072/70‑1 (MQ=255)
gTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATAtt < 1:533451/67‑1 (MQ=255)
gTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATAtt < 1:2617158/67‑1 (MQ=255)
ttGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGtttt < 1:3513855/57‑1 (MQ=255)
ttGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTa < 1:1887573/40‑1 (MQ=255)
ttGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGttt > 1:1501310/1‑56 (MQ=255)
tGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACt > 1:2737794/1‑71 (MQ=255)
gccgccCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACtt > 1:3255473/1‑71 (MQ=255)
cgccCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTg < 1:52316/71‑1 (MQ=255)
gccCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGt < 1:227518/71‑1 (MQ=255)
gccCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCtt < 1:2869195/41‑1 (MQ=255)
cGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGc > 1:247352/1‑39 (MQ=255)
cGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTtata < 1:1398032/55‑1 (MQ=255)
gAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGtt < 1:607589/66‑1 (MQ=255)
gAACCCTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTtatat > 1:711741/1‑70 (MQ=255)
aaCCCTTTCGGCACCGAGAAACC‑CTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAg > 1:453588/1‑71 (MQ=255)
cTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACttt < 1:2801139/58‑1 (MQ=255)
cTTTCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCt > 1:3746158/1‑71 (MQ=255)
tttCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCt < 1:96208/43‑1 (MQ=255)
tttCGGCACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCtt > 1:3797425/1‑71 (MQ=255)
tCGGCACCGAGAAACCACTTAAATCTTGCATTGGt < 1:1379527/35‑1 (MQ=255)
tCGGCACCGAGAAACCACTTAAATCTTGCATTGGt < 1:3916651/35‑1 (MQ=255)
cGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTc < 1:1384997/70‑1 (MQ=255)
cACCGAGAAACCGCTTAAATCTTGCATTGGTTTTCCTTATAtt < 1:3735599/43‑1 (MQ=255)
aCCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCtt > 1:1469476/1‑71 (MQ=255)
aCCGAGAAACCACTTAAATCTTGCATTGGTTTTCC‑TATATTCAGACTTTGTTATATAAGGCTTTCGTCtt > 1:3888751/1‑70 (MQ=255)
ccGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACt < 1:1809460/47‑1 (MQ=255)
cGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGt < 1:2581520/50‑1 (MQ=255)
cGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCttt > 1:3933833/1‑70 (MQ=255)
cGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCttt > 1:3483169/1‑70 (MQ=255)
gagaAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTtata < 1:2249493/53‑1 (MQ=255)
gagaAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGtt > 1:2928023/1‑50 (MQ=255)
gagaAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCttt > 1:975364/1‑69 (MQ=255)
gagaAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTATTATATAAGGCTTTCGTCttt > 1:1210526/1‑69 (MQ=255)
agaAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAg < 1:3662616/71‑1 (MQ=255)
agaAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAg > 1:1618926/1‑71 (MQ=255)
gaAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAgg > 1:2623107/1‑71 (MQ=255)
gaAACCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAgg > 1:1124306/1‑71 (MQ=255)
gaAACCACTTAAATCTTGCATTTGTTTTCCTTATATTCAGACTTTGTTATATAAgg > 1:2603864/1‑56 (MQ=255)
gaAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAgg > 1:1670342/1‑56 (MQ=255)
aaaCCGCTTAAATCTTGCATTGGTTTTCCTTATAtt < 1:3623428/36‑1 (MQ=255)
aaCCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGgta < 1:2440866/71‑1 (MQ=255)
aCCGCTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTtatat < 1:437787/49‑1 (MQ=255)
|
GCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCACTTAAATCTTGCATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTA > minE/1337418‑1337546
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
