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 |
2,615,665 |
C→T |
58.5% |
R70R (CGC→CGT) |
yhhS → |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,615,665 | 0 | C | T | 58.5%
| 23.2
/ 56.2
| 77 | R70R (CGC→CGT) | yhhS | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base C (18/14); new base T (20/25); total (38/39) |
| Fisher's exact test for biased strand distribution p-value = 3.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.56e-01 |
CTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGACCCAAAAAGATTGT > minE/2615602‑2615712
|
cTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCa < 1:3258206/69‑1 (MQ=255)
cTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCa < 1:653407/69‑1 (MQ=255)
tttAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCa < 1:852843/68‑1 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGag > 1:368657/3‑68 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:2056545/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:365555/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:3046627/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:3024735/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:3008495/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:53072/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:560571/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:577614/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:613998/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:226824/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:809114/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:1728404/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:117496/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:1207567/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:1372916/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:1505807/3‑69 (MQ=255)
cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:1553847/3‑69 (MQ=255)
cattCTCGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc > 1:1932402/3‑69 (MQ=255)
cattGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGACGt > 1:2216959/4‑69 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:778474/1‑46 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt < 1:1014519/46‑1 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:3165208/1‑46 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:1039054/1‑46 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt < 1:871368/46‑1 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:1575281/1‑46 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:12463/1‑46 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt < 1:407489/46‑1 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt < 1:799211/46‑1 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:2724537/1‑46 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:2414441/1‑46 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt < 1:2313402/46‑1 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt < 1:2197001/46‑1 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:2080964/1‑46 (MQ=255)
aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt > 1:729976/1‑46 (MQ=255)
aTCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTgaga > 1:1344577/1‑69 (MQ=255)
aTCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGa > 1:1954054/1‑69 (MQ=255)
aTCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGa > 1:1462437/1‑69 (MQ=255)
aTCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGa > 1:673719/1‑69 (MQ=255)
aTCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGa > 1:1560274/1‑69 (MQ=255)
aTCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGa > 1:392278/1‑69 (MQ=255)
aTCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGa > 1:1995767/1‑69 (MQ=255)
aTCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGa > 1:3361863/1‑69 (MQ=255)
aGCCTGCAATATTTCGCCACCTTTCTGAGCCGCCCTCATGCCGGACGTTACGcc < 1:2946571/54‑1 (MQ=255)
aGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATTCCGGACGTTACGcc < 1:1007633/54‑1 (MQ=255)
aGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGcc < 1:1010671/54‑1 (MQ=255)
aGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGcc < 1:2573600/54‑1 (MQ=255)
aGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGcc < 1:3336749/54‑1 (MQ=255)
tttCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGACCCAAAAAGATTgt > 1:1861467/1‑69 (MQ=255)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:2713065/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:995890/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:978803/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:1728645/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:1833598/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:1928040/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:199686/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:766239/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:204677/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:712440/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:2573842/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:2864871/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:2890691/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:519413/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:483466/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:430104/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:423129/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:2951211/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:3071570/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:3094026/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:3198393/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:3431545/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:3371701/52‑1 (MQ=37)
ccTTGCTGAGCCGTCCTCATGCCGGACGTTACGCCGATTTACTGGGACCaaa < 1:3234334/52‑1 (MQ=37)
cTTGCTGAGCCGTCCTCATGCCGGACGTTACCCCGATTTACTGGGACCaaa < 1:2433778/51‑1 (MQ=255)
|
CTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGTTACGCCGATTCGCTGGGACCCAAAAAGATTGT > minE/2615602‑2615712
|
| 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
