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 |
826,710 |
G→A |
46.0% |
Q369Q (CAG→CAA) |
ychP → |
predicted invasin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 826,710 | 0 | G | A | 46.0%
| 5.1
/ 38.9
| 50 | Q369Q (CAG→CAA) | ychP | predicted invasin |
| Reads supporting (aligned to +/- strand): ref base G (18/9); new base A (2/21); total (20/30) |
| Fisher's exact test for biased strand distribution p-value = 3.28e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 |
TGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCAGGGGCAGCGTGTC > minE/826649‑826779
|
tGACGCCGGGCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACgg > 1:382767/1‑67 (MQ=255)
tGACGCCGGGCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACgg > 1:505581/1‑67 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:99022/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:2491143/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:2976427/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:2080192/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:193133/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:181466/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:481414/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:15820/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:689717/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:736510/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1462277/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1337415/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:739380/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:805196/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:888520/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1187586/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1173152/69‑1 (MQ=255)
ggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1443295/68‑1 (MQ=255)
ggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:501578/68‑1 (MQ=255)
caAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:400362/62‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:3368590/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:3091494/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:1022221/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:2396266/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:2245266/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:168860/69‑1 (MQ=255)
cTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCAc > 1:1007731/1‑52 (MQ=255)
cTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:2232299/57‑1 (MQ=255)
cTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCt > 1:3156821/1‑64 (MQ=255)
cTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTgtggt > 1:2899710/1‑69 (MQ=255)
cTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTgtggt > 1:1485727/1‑69 (MQ=255)
cTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTgtggt < 1:1714367/69‑1 (MQ=255)
ggACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:909227/40‑1 (MQ=38)
cATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATa > 1:2923798/1‑68 (MQ=255)
cATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATa > 1:1597587/1‑68 (MQ=255)
cATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATa > 1:1297821/1‑68 (MQ=255)
cATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATa > 1:1273617/1‑68 (MQ=255)
cATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATa > 1:2340425/1‑68 (MQ=255)
gCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCa > 1:2131558/1‑69 (MQ=255)
gCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCa > 1:3433034/1‑69 (MQ=255)
gCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCa > 1:1787162/1‑69 (MQ=255)
gCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCa > 1:2179780/1‑69 (MQ=255)
gCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCa > 1:1689936/1‑69 (MQ=255)
gCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCa > 1:1226297/1‑69 (MQ=255)
gCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCAGGGGCAGCg > 1:563377/1‑69 (MQ=255)
gCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCAGGGGCAGCg > 1:654283/1‑69 (MQ=255)
gCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCAGGGGCAGCg > 1:3060701/1‑69 (MQ=255)
aGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGT‑GT‑‑AAGATAACCAGGGGCAGCGTGtc < 1:1540209/68‑1 (MQ=255)
|
TGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCGATTGTCTGTGGTGGTGGAAGATAACCAGGGGCAGCGTGTC > minE/826649‑826779
|
| 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
