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 |
1,402,418 |
A→G |
40.6% |
A87A (GCA→GCG) |
rtn → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,402,418 | 0 | A | G | 40.6%
| 22.6
/ 44.3
| 64 | A87A (GCA→GCG) | rtn | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (17/21); new base G (9/17); total (26/38) |
| Fisher's exact test for biased strand distribution p-value = 4.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACTGACCGGCTCCAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCA > minE/1402350‑1402478
|
actGACCGGCTCCAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCa > 1:210335/1‑69 (MQ=255)
cGGCTCCAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCC‑‑CGCAGCGTTTAg < 1:2934996/69‑1 (MQ=255)
gCTCCAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGTAGCGTTTAg < 1:761154/69‑1 (MQ=255)
gCTCCAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAg < 1:1422403/69‑1 (MQ=255)
gCTCCAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAg < 1:1989237/69‑1 (MQ=255)
gCTCCAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAg < 1:1751630/69‑1 (MQ=255)
cAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATg > 1:1345228/1‑69 (MQ=255)
cAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATg > 1:58249/1‑69 (MQ=255)
cAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATg > 1:2722140/1‑69 (MQ=255)
cAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATg > 1:3295749/1‑69 (MQ=255)
cAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGACCGCGCAGCGTTTAGCATg > 1:3022856/1‑69 (MQ=255)
gCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATg < 1:2417438/67‑1 (MQ=255)
cGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATg < 1:2854745/69‑1 (MQ=255)
cGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATg < 1:1348352/69‑1 (MQ=255)
cGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATg < 1:1625183/69‑1 (MQ=255)
cGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATg < 1:209033/69‑1 (MQ=255)
cGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATg < 1:2619667/69‑1 (MQ=255)
gCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATg < 1:56099/68‑1 (MQ=255)
gACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCg < 1:3393751/69‑1 (MQ=255)
gACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCg < 1:3088627/69‑1 (MQ=255)
gACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCg < 1:1281992/69‑1 (MQ=255)
gACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCg < 1:1119170/69‑1 (MQ=255)
cAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGa > 1:2771197/1‑43 (MQ=255)
cAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGt > 1:3354490/1‑65 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATTAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1710428/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:3284109/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1054084/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:495064/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:500187/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:2891160/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:893066/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:975863/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:2409450/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1199642/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:2332472/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1385246/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:2019109/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1859630/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1890875/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1994782/69‑1 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:828341/68‑1 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGAt > 1:287666/1‑68 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGAt > 1:2924645/1‑68 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGAt > 1:691099/1‑68 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGAt > 1:3326619/1‑68 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACATTTGTGCTGGTGAAAGAt > 1:240433/1‑68 (MQ=255)
ccccGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaaa > 1:993020/1‑69 (MQ=255)
ccccGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaaa > 1:892000/1‑69 (MQ=255)
ccccGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCAGAACGTTTGTGCTGGTGaaa > 1:1037802/1‑61 (MQ=255)
ccccGAACTGACCGCCCGCGCAGCGTTTAGCATCAATGTCAGa > 1:2019425/1‑43 (MQ=38)
ccccGAACTGACCGCCCGCGCAGCGTTTAGAATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaa > 1:1202317/1‑68 (MQ=255)
ccGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaaaaa < 1:2298991/69‑1 (MQ=255)
cGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaaaaa < 1:3196101/68‑1 (MQ=255)
gAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACa < 1:682522/69‑1 (MQ=255)
gAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACa < 1:2618239/69‑1 (MQ=255)
gAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACa < 1:2700279/69‑1 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:1933019/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:1589031/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:2370547/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:2792898/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:462052/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:954643/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:325034/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:1893460/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAAGGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGt > 1:1118514/1‑66 (MQ=255)
|
ACTGACCGGCTCCAGCCGCTGACCTTAGATACCTGCCAGCAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCA > minE/1402350‑1402478
|
| 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
