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 |
|
A1 F1 I2 R1
|
730 |
35.1 |
2107516 |
91.4% |
1926269 |
80.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,509,874 |
T→C |
H368R (CAT→CGT) |
yhfX ← |
putative PLP‑binding protein YhfX |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,509,874 | 0 | T | C | 96.8%
| 99.7
/ ‑3.9
| 31 | H368R (CAT→CGT) | yhfX | putative PLP‑binding protein YhfX |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (15/15); total (15/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 |
CACAAATCGCGCCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGATGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGCACCACTGCACTGCT > NC_000913/3509799‑3509950
|
cacaAATCGCGCCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATa < 2:671678/81‑1 (MQ=255)
aTCGCGCCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGa < 1:671680/81‑1 (MQ=255)
aTCGCGCCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGa < 1:671679/81‑1 (MQ=255)
tCGCGCCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGac < 1:671681/81‑1 (MQ=255)
cgcgCCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGaca > 1:671750/1‑81 (MQ=255)
cgcgCCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGaca > 1:671746/1‑81 (MQ=255)
gcgcCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGacac > 2:671733/1‑81 (MQ=255)
cgcCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGATGAATACCGGACAcc < 1:671682/81‑1 (MQ=255)
cgcCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGacac > 1:671751/1‑80 (MQ=255)
aCGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGcacca > 1:671743/1‑81 (MQ=255)
gagagTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTAc > 1:671730/1‑81 (MQ=255)
agTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACggg > 1:671764/1‑81 (MQ=255)
tttCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTg < 1:671683/81‑1 (MQ=255)
cAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACaa < 2:671685/81‑1 (MQ=255)
cAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACa < 2:671684/80‑1 (MQ=255)
aaGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACaaa < 1:671686/81‑1 (MQ=255)
tGTCATAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCt > 2:671741/1‑81 (MQ=255)
aTAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCtgcgt < 2:671687/81‑1 (MQ=255)
aTAACGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCtgcg < 2:671688/80‑1 (MQ=255)
aCGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCtgcgtgc > 1:671748/1‑80 (MQ=255)
aCGACCGACGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCtgcgtgc < 2:671689/80‑1 (MQ=255)
gaccgacGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGaa < 1:671690/81‑1 (MQ=255)
gaccgacGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGa > 2:671763/1‑80 (MQ=255)
accgacGATTTCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGaa > 1:671749/1‑80 (MQ=255)
ttCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGcac > 1:671745/1‑81 (MQ=255)
tCCGGTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTGCGGGTGACAAAAATCTGCGTGCGAAAACAGAGcac > 2:671740/1‑80 (MQ=255)
gTTCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGCACcactg > 1:671737/1‑81 (MQ=255)
ttCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGCACcactgc < 2:671691/81‑1 (MQ=255)
tCGCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGCACcactgca > 2:671755/1‑81 (MQ=255)
gCCACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGCACcactgcact < 1:671692/81‑1 (MQ=255)
ccACGACGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGCACcactgcactg < 2:671693/81‑1 (MQ=255)
cgacgaATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGCACCACTGCACTGCt > 2:671760/1‑80 (MQ=255)
|
CACAAATCGCGCCATTACGCCCCCAGAGAGTTTCCAAGACTGTCATAACGACCGACGATTTCCGGTTCGCCACGATGAATACCGGACACCAGCACCACATCGCTACGGGTGACAAAAATCTGCGTGCGAAAACAGAGCACCACTGCACTGCT > NC_000913/3509799‑3509950
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
