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 |
|
A21 F63 I0 R1
|
37 |
31.8 |
718920 |
95.7% |
688006 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,343,438 |
C→T |
40.1% |
intergenic (+114/+250) |
USA300HOU_RS11955 → / ← aldC_1 |
65 kDa membrane protein/Alpha‑acetolactate decarboxylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,343,438 | 0 | C | T | 40.1%
| 6.9
/ 19.5
| 20 | intergenic (+114/+250) | USA300HOU_RS11955/aldC_1 | 65 kDa membrane protein/Alpha‑acetolactate decarboxylase |
| Reads supporting (aligned to +/- strand): ref base C (7/5); new base T (2/6); total (9/11) |
| Fisher's exact test for biased strand distribution p-value = 1.97e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.66e-01 |
GATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAG > USA300TCH1516_ALE/2343303‑2343566
|
gATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAg < 2:48877/141‑1 (MQ=255)
aTACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGt < 2:132917/141‑1 (MQ=255)
tACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTa > 1:292200/1‑141 (MQ=255)
tAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCCCCGATAAAGTGTCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAg < 1:276195/141‑1 (MQ=255)
aatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTAcc > 1:96960/1‑141 (MQ=255)
aaTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTta < 2:108522/141‑1 (MQ=255)
ttATAGGTCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTa < 2:260503/141‑1 (MQ=255)
gggCAAGCGCTGAAAAATAGGCGTATGTCTTTTTAGATATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGAAACAGATTAGCCTATACAATAGTAAATATTAAAAGAGTGTGTACCACAAAATATAATCTAAACaa > 2:27822/1‑140 (MQ=255)
aGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAg < 1:44984/141‑1 (MQ=255)
aGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAg > 1:340556/1‑141 (MQ=255)
aGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAg > 1:91/1‑141 (MQ=255)
cTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTCTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCaaa > 1:159954/1‑141 (MQ=255)
tttGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTgg < 1:223530/141‑1 (MQ=255)
aTTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAAGATAACAGCAAATCTCGAATATCGGGTACCTAATAAATcac > 1:298279/1‑139 (MQ=255)
tGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCt < 1:126834/141‑1 (MQ=255)
cTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCact > 2:252309/1‑141 (MQ=255)
gTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCactact < 2:292200/141‑1 (MQ=255)
aaaTTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCTTCactattag < 2:266640/141‑5 (MQ=255)
gttgttTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTg < 2:96960/141‑1 (MQ=255)
gATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAAAATAACAGCAACTCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTCATAGTGAAGGGATTTCTTTTATTACTTAg > 2:280016/1‑141 (MQ=255)
|
GATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAG > USA300TCH1516_ALE/2343303‑2343566
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
