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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,235,640:1 |
+A |
53.8% |
coding (655/1542 nt) |
nhaB ← |
sodium:proton antiporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,235,640 | 1 | . | A | 53.8%
| 11.5
/ 19.6
| 13 | coding (655/1542 nt) | nhaB | sodium:proton antiporter |
| Reads supporting (aligned to +/- strand): ref base . (3/3); new base A (3/4); total (6/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGCGCAGGAAGAAATCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCAC‑CATGGTCATTACGCCGCCTAATGCGGTGCCGACACCGGCATGCATCATCAGG > W3110S.gb/1235571‑1235692
|
tGCGCAGGAAGAAATCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCccaca < 1:1176519/71‑2 (MQ=255)
cgcAGGAAGAAATCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCccacaca > 1:1261863/1‑68 (MQ=255)
cgcAGGAAGAAATCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCccacaca > 1:527033/1‑68 (MQ=255)
cgcAGGAAGAAATCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCccacaca > 1:2064394/1‑68 (MQ=255)
aagaaATCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCAC‑CATGGTCAt < 1:2300898/71‑1 (MQ=255)
agaaATCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCACACATGGTCAt > 1:1180203/1‑71 (MQ=255)
aaTCGCAAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCAC‑CATGGTCATTAcg > 1:2120840/1‑71 (MQ=255)
tCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCAC‑CATGGTCAt < 1:792196/65‑1 (MQ=255)
gCCAAAATGCCAGCCAGCCGCTTTAGCGTTGATCAGGTTCTGTGGTTCGCCCACACATGGTCATTAcgccg > 1:140318/1‑71 (MQ=255)
cAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCAC‑CATGGTCATTAc < 1:82725/64‑1 (MQ=255)
ccagccagCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCACACATGGTCATTACGCCGCCTAATGc < 1:164040/70‑1 (MQ=255)
ccagccagCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCACACATGGTCATTACGCCGCCTAATGc < 1:1515119/70‑1 (MQ=255)
cagccGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCACACATGGTCATTACGCCGCCTAATGCGGTGcc < 1:1973019/71‑1 (MQ=255)
cAGGTTCTGTGGTTCGCCCACACATGGTCATTACGCCGCCTAATGCGGTCCCGaca > 1:2526245/1‑56 (MQ=255)
cAGGTTCTGTGGTTCGCCCAC‑CATGGTCATTACGCCGCCTAATGCGGTGCCGACACCGGCATGcatcat > 1:739730/1‑69 (MQ=255)
tCTGTGGTTCGCCCAC‑CATGGTCATTACGCCGCCTAATGCGGTGCCGACACCGGCATGCATCATCAgg > 1:2659397/1‑68 (MQ=255)
gTTCGCCCACACATGGTCATTACGCCGCCTAATGc < 1:2005404/35‑1 (MQ=37)
|
TGCGCAGGAAGAAATCGCCAAAATGCCAGCCAGCCGCTTTAGCGATGATCAGGTTCTGTGGTTCGCCCAC‑CATGGTCATTACGCCGCCTAATGCGGTGCCGACACCGGCATGCATCATCAGG > W3110S.gb/1235571‑1235692
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
