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 |
|
A5 F21 I0 R1
|
148 |
22.8 |
1772010 |
97.0% |
1718849 |
61.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,841,531 |
G→A |
40.9% |
R57* (CGA→TGA) |
hycI ← |
protease involved in processing C‑terminal end of HycE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,841,531 | 0 | G | A | 40.9%
| 11.7
/ 21.4
| 22 | R57* (CGA→TGA) | hycI | protease involved in processing C‑terminal end of HycE |
| Reads supporting (aligned to +/- strand): ref base G (5/8); new base A (6/3); total (11/11) |
| Fisher's exact test for biased strand distribution p-value = 3.87e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01 |
GGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATCA > W3110S.gb/2841467‑2841593
|
gggTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCgg > 1:439831/1‑71 (MQ=255)
gatgCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGtt > 1:968889/1‑71 (MQ=255)
cGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCAc < 1:954133/70‑1 (MQ=255)
ggATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACg > 1:542354/1‑70 (MQ=255)
cGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGcgac > 1:1123511/1‑70 (MQ=255)
gCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGAt < 1:1061447/55‑1 (MQ=255)
ccccATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGtttt < 1:291715/71‑1 (MQ=255)
ccccATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGtttt < 1:761406/71‑1 (MQ=255)
ccATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTcc < 1:1481428/71‑1 (MQ=255)
ccATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTcc > 1:698950/1‑71 (MQ=255)
atatCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCgg < 1:292945/71‑1 (MQ=255)
ccGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGtttt > 1:464266/1‑63 (MQ=255)
ccGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTc > 1:487939/1‑64 (MQ=255)
ccGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTc > 1:1509970/1‑64 (MQ=255)
cGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTgcgt < 1:507441/71‑2 (MQ=255)
ggCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTAc > 1:736151/1‑71 (MQ=255)
tCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGttt < 1:1014711/54‑1 (MQ=255)
cGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCgg > 1:781678/1‑58 (MQ=255)
aCAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGt < 1:446785/70‑1 (MQ=255)
cAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTc > 1:836558/1‑70 (MQ=255)
tCAGCAGTCATGTCGGGCGCAGTTCACGGATAGcgacg < 1:211849/38‑1 (MQ=255)
agcagTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATca < 1:1643852/70‑1 (MQ=255)
|
GGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATCA > W3110S.gb/2841467‑2841593
|
| 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
