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 |
2,572,487 |
A→G |
35.6% |
intergenic (+1255/‑524) |
yibH → / → ysaB |
hypothetical protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,572,487 | 0 | A | G | 35.6%
| 51.7
/ 55.7
| 59 | intergenic (+1255/‑524) | yibH/ysaB | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (19/19); new base G (4/17); total (23/36) |
| Fisher's exact test for biased strand distribution p-value = 2.64e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01 |
TCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAG > minE/2572424‑2572549
|
tCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCa < 1:3526062/68‑1 (MQ=255)
tCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCa < 1:2932921/68‑1 (MQ=255)
aGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTAt < 1:1919011/71‑1 (MQ=255)
aGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTAt > 1:481462/1‑71 (MQ=255)
ggTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTAtt < 1:702734/71‑1 (MQ=255)
ggTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTAtt < 1:2185451/71‑1 (MQ=255)
tttCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTta > 1:2243897/1‑70 (MQ=255)
cTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATaa < 1:1231828/70‑1 (MQ=255)
ttgcttgcTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAAtg < 1:2860020/70‑1 (MQ=255)
ttgcttgcTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAt < 1:3114016/69‑1 (MQ=255)
ttgcttgcTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAt < 1:2163358/69‑1 (MQ=255)
tgcttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgtg > 1:2458049/1‑71 (MQ=255)
tgcttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgtg > 1:3074519/1‑71 (MQ=255)
gcttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgtg < 1:3128081/70‑1 (MQ=255)
cttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATgtgt < 1:2579303/70‑1 (MQ=255)
cttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATgtgt < 1:2844264/70‑1 (MQ=255)
gctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTAc < 1:1807048/69‑1 (MQ=255)
tCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCt < 1:2673480/51‑1 (MQ=255)
ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCAt > 1:3862362/1‑47 (MQ=255)
ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCAt > 1:2626533/1‑47 (MQ=255)
ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACggg < 1:943008/71‑1 (MQ=255)
ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACggg > 1:110121/1‑71 (MQ=255)
ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACggg > 1:225569/1‑71 (MQ=255)
ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACgg < 1:2573287/70‑1 (MQ=255)
gggTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAAt < 1:3179684/57‑1 (MQ=255)
aTTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGattat < 1:3293257/70‑1 (MQ=255)
aTTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGattatt < 1:3602724/71‑1 (MQ=255)
ttAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAAtgt < 1:970482/53‑1 (MQ=255)
ttAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAAtgt < 1:3460221/53‑1 (MQ=255)
ttAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATaa < 1:1889891/49‑1 (MQ=255)
ttAACATTCCAACTCCATAGGCCTTGACGTATTGGCCATCTAt < 1:3566574/43‑1 (MQ=255)
aaCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt > 1:3910793/1‑70 (MQ=255)
aCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa > 1:3568944/1‑71 (MQ=255)
aTTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtata < 1:3024226/43‑1 (MQ=255)
aTTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtata < 1:1026229/43‑1 (MQ=255)
aTTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACa < 1:2710899/71‑1 (MQ=255)
ccAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTg > 1:3128743/1‑71 (MQ=255)
cAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGc < 1:3821712/71‑1 (MQ=255)
cTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCat > 1:1617671/1‑70 (MQ=255)
ccATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCatat > 1:3306258/1‑70 (MQ=255)
cATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtatta < 1:2103596/71‑1 (MQ=255)
cATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtatt < 1:629199/70‑1 (MQ=255)
tAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa > 1:2080106/1‑57 (MQ=255)
tAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtattat > 1:357718/1‑70 (MQ=255)
tAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtattat > 1:3195734/1‑70 (MQ=255)
tAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtattat > 1:352958/1‑70 (MQ=255)
aGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt > 1:2001804/1‑54 (MQ=255)
ggCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATAttatta < 1:1669251/70‑1 (MQ=255)
gCCTTGAGGTATTAGCCATCTATTTATAAATGTGTAc < 1:520280/37‑1 (MQ=255)
cTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGatta < 1:991357/46‑1 (MQ=255)
cTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAg < 1:3389910/71‑1 (MQ=255)
cTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCa < 1:1772337/70‑1 (MQ=255)
tGAGGTATTAGCCATCTATTTATAAATGTGTACAACggg > 1:530101/1‑39 (MQ=255)
tGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAg > 1:1342521/1‑69 (MQ=255)
gAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAg > 1:2592808/1‑71 (MQ=255)
gAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa > 1:2223826/1‑49 (MQ=255)
gAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGa < 1:1864573/69‑1 (MQ=255)
gAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAg > 1:3287971/1‑71 (MQ=255)
aTTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa < 1:2024553/44‑1 (MQ=255)
|
TCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAG > minE/2572424‑2572549
|
| 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
