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 |
2,561,298 |
C→A |
31.9% |
A117A (GCG→GCT) |
lldD ← |
L‑lactate dehydrogenase, FMN‑linked |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,561,298 | 0 | C | A | 31.9%
| 85.6
/ 45.2
| 72 | A117A (GCG→GCT) | lldD | L‑lactate dehydrogenase, FMN‑linked |
| Reads supporting (aligned to +/- strand): ref base C (25/24); new base A (4/19); total (29/43) |
| Fisher's exact test for biased strand distribution p-value = 9.44e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01 |
ACGCATAAAGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACGGAATAC > minE/2561235‑2561350
|
aCGCATAAAGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGAc < 1:1422024/69‑1 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGACCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:1061923/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGActtcttaa > 1:494330/1‑67 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:1021775/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:508111/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:1595059/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:553033/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:1434428/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:2159444/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:581391/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:3131604/1‑69 (MQ=255)
aaGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCa > 1:2875697/1‑69 (MQ=255)
cgcgCAGCACATAAAGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCAATCGGGCaaa > 1:3017741/1‑69 (MQ=255)
cgcgCAGCACATAAAGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCAATCGGGCaaa > 1:1139961/1‑69 (MQ=255)
cgcgCAGCACATAAAGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCAATCGGGCaaa > 1:1108988/1‑69 (MQ=255)
cgcgCAGCACATAAAGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCAATCGGGCaaa > 1:2001948/1‑69 (MQ=255)
aCATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAAcc > 1:2715339/1‑69 (MQ=255)
aCATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAAcc > 1:1826899/1‑69 (MQ=255)
aCAAAAAGCTGGAACCACATAGGGCGCTTGATGGCTGGCGCGACTACTTCa > 1:970564/1‑51 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAAc > 1:992167/1‑67 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:2223223/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:264171/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:2084687/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:1843752/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:1688708/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:907533/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:1279038/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:1307711/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:1415328/1‑69 (MQ=255)
cATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCg > 1:444178/1‑69 (MQ=255)
tAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTc < 1:447031/69‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:3393577/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:3351265/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:3399499/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:413644/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:3159494/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:3048944/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:588844/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:6092/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:2837428/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:416870/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:1027620/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:1234405/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:125531/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:2531921/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:1202310/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:1621022/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:164616/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:2623845/46‑1 (MQ=255)
aaGCTGGAACCACATCGGACGTTTGATAGCCGGAGCCACTTCTTCa < 1:208158/46‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:2756610/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:1369561/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:1643943/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:1814554/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:2135558/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:3330187/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:2292282/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:2325415/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:2331874/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:2921348/68‑1 (MQ=255)
aCCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:922970/68‑1 (MQ=255)
caTTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACgg < 1:214829/69‑1 (MQ=255)
caTTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACgg < 1:1580241/69‑1 (MQ=255)
caTTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACgg < 1:260521/69‑1 (MQ=255)
caTTGGGAGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACgg < 1:2408595/69‑1 (MQ=255)
gcgcTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACGGAATAc < 1:1096677/68‑1 (MQ=255)
gcgcTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACGGAATAc < 1:2004935/68‑1 (MQ=255)
gcgcTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACGGAATAc < 1:897238/68‑1 (MQ=255)
gcgcTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACGGAATAc < 1:1614337/68‑1 (MQ=255)
gcgcTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACGGAATAc < 1:2888480/68‑1 (MQ=255)
gcgcTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACGGAATAc < 1:2775950/68‑1 (MQ=255)
gcTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTa < 1:1033305/56‑1 (MQ=255)
|
ACGCATAAAGCCGCGATCGCGCAGTACATAAAGCTGGAACCACATTGGGCGCTTGATGGCTGGCGCGACTTCTTCAATCGGGCAAACGGAAACCGTCGAGAGAGTAAACGGAATAC > minE/2561235‑2561350
|
| 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
