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 |
1,367,294 |
G→A |
28.6% |
A49A (GCC→GCT) |
yohG ← |
predicted outer membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,367,294 | 0 | G | A | 28.6%
| 76.9
/ 29.4
| 73 | A49A (GCC→GCT) | yohG | predicted outer membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (18/34); new base A (7/14); total (25/48) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.71e-01 |
CTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCG > minE/1367229‑1367343
|
cTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGc < 1:2621411/68‑1 (MQ=255)
cTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGc < 1:1231726/68‑1 (MQ=255)
cTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGc > 1:1336307/1‑68 (MQ=255)
cTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGc < 1:2580634/68‑1 (MQ=255)
cTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGc > 1:2651900/1‑68 (MQ=255)
cTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGc > 1:670987/1‑68 (MQ=255)
agccagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTa < 1:1985945/67‑1 (MQ=255)
agccagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTa < 1:306847/67‑1 (MQ=255)
agccagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTa < 1:3017029/67‑1 (MQ=255)
agccagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTa < 1:478759/67‑1 (MQ=255)
agccagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTa < 1:2951295/67‑1 (MQ=255)
agccagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTa < 1:609881/67‑1 (MQ=255)
agccagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTa < 1:1295082/67‑1 (MQ=255)
agccagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTa < 1:1119841/67‑1 (MQ=255)
cagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTc > 1:2571792/1‑69 (MQ=255)
cagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTc > 1:1999167/1‑69 (MQ=255)
cagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTc > 1:26417/1‑69 (MQ=255)
cagcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTc > 1:1635688/1‑69 (MQ=255)
ggTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCtt > 1:1734511/1‑69 (MQ=255)
ggTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCtt > 1:1812491/1‑69 (MQ=255)
gTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:2600200/69‑1 (MQ=255)
gTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:315217/69‑1 (MQ=255)
gTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:2348240/69‑1 (MQ=255)
gTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:2259338/69‑1 (MQ=255)
gTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:1499588/69‑1 (MQ=255)
gTTTGCTCGCGGTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:2481103/69‑1 (MQ=255)
tttGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGGGGGCAGTAACCTCCGACCGATTCttt < 1:3362507/68‑1 (MQ=255)
tttGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:2107833/68‑1 (MQ=255)
tttGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:1958282/68‑1 (MQ=255)
tttGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:1929746/68‑1 (MQ=255)
tttGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:1775409/68‑1 (MQ=255)
tttGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTc > 1:554031/1‑69 (MQ=255)
cgcgTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCttt < 1:1515687/62‑1 (MQ=255)
ccgccgCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGata > 1:405856/1‑65 (MQ=255)
ccgccgCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGata > 1:1424960/1‑65 (MQ=255)
ccgccgCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGata > 1:2425580/1‑65 (MQ=255)
ccgccgCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGata > 1:813645/1‑65 (MQ=255)
ccgccgCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGata > 1:2586260/1‑65 (MQ=255)
ccgccgCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGat > 1:1221504/1‑64 (MQ=255)
cgccgcCCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTc < 1:428912/52‑1 (MQ=39)
cgccgcCCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTc < 1:869242/52‑1 (MQ=39)
cgccgcCCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTc < 1:3260050/52‑1 (MQ=39)
cgccgcCCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTc < 1:920786/52‑1 (MQ=39)
cgccgcCCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTc < 1:1507720/52‑1 (MQ=39)
cgccgcCCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTc < 1:11523/52‑1 (MQ=39)
cgccgcCCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTc < 1:2312007/52‑1 (MQ=39)
cgccgcCCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTc < 1:2202137/52‑1 (MQ=39)
ccgccCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGAt < 1:2121679/69‑1 (MQ=255)
ccgccCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGAt < 1:136593/69‑1 (MQ=255)
ccgccCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGAt < 1:821546/69‑1 (MQ=255)
ccgccCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGAt < 1:1438883/69‑1 (MQ=255)
ccgccCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGAt < 1:1698687/69‑1 (MQ=255)
ccgccCGTGCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGAt < 1:593511/69‑1 (MQ=255)
cGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAg < 1:1370024/69‑1 (MQ=255)
cGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAg < 1:3211109/69‑1 (MQ=255)
gCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGccc > 1:2138473/1‑69 (MQ=255)
gCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGccc > 1:919889/1‑69 (MQ=255)
gCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGccc > 1:1450361/1‑69 (MQ=255)
gCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGccc > 1:1452306/1‑69 (MQ=255)
gCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGccc > 1:1454265/1‑69 (MQ=255)
gCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGccc > 1:1598978/1‑69 (MQ=255)
gCTTTAACCGTACCCAGGCGAGCAGTAATCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGcc > 1:3136771/1‑68 (MQ=255)
cTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCccg > 1:618003/1‑69 (MQ=255)
cTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCccg > 1:1763297/1‑69 (MQ=255)
gCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:2747803/41‑1 (MQ=255)
gCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:554823/41‑1 (MQ=255)
gCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:366459/41‑1 (MQ=255)
gCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:801845/41‑1 (MQ=255)
gCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:3165156/41‑1 (MQ=255)
gCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:3153517/41‑1 (MQ=255)
gCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:1819694/41‑1 (MQ=255)
gCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:2730888/41‑1 (MQ=255)
gCGGGAAGTAACCTCCGCCCGATTCTTTCCCCAGATATCga < 1:548513/41‑1 (MQ=255)
|
CTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCG > minE/1367229‑1367343
|
| 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
