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 |
|
A68 F1 I1 R1
|
17 |
56.4 |
3914180 |
96.2% |
3765441 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,762,214 |
A→G |
Y67H (TAT→CAT) |
rpoS ← |
RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,762,214 | 0 | A | G | 97.7%
| 177.8
/ ‑3.9
| 44 | Y67H (TAT→CAT) | rpoS | RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (28/15); total (28/16) |
| Fisher's exact test for biased strand distribution p-value = 3.64e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
CGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTC > REL606/2762141‑2762283
|
cgAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGAc < 2:1427015/76‑1 (MQ=255)
cgAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGAc > 2:1646362/1‑76 (MQ=255)
agGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAAt > 2:260221/1‑76 (MQ=255)
cGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAAtctc > 1:1524177/1‑76 (MQ=255)
cGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAAtctc < 2:143799/76‑1 (MQ=255)
gACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCa < 1:1489620/76‑1 (MQ=255)
aCATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCAc < 2:172153/76‑1 (MQ=255)
cATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCAcc > 2:1779658/1‑76 (MQ=255)
aTCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCa > 1:253489/1‑76 (MQ=255)
ctcCACGCGGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAg < 1:1739816/76‑1 (MQ=255)
ctcCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAg < 1:739045/76‑1 (MQ=255)
ccACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGt < 1:297975/76‑1 (MQ=255)
ccACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGt < 1:740600/76‑1 (MQ=255)
ccACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGt < 2:307149/76‑1 (MQ=255)
ccACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGt > 2:1082051/1‑76 (MQ=255)
cACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTa > 1:775082/1‑76 (MQ=255)
cACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTa > 2:359226/1‑76 (MQ=255)
cgcgACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGt > 2:1613228/1‑76 (MQ=255)
gcgACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTc < 1:482692/76‑1 (MQ=255)
aaaaTAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAac > 2:1897849/1‑76 (MQ=255)
aaaaTAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAac > 1:1949157/1‑76 (MQ=255)
aaaaTAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAac > 1:1192664/1‑76 (MQ=255)
aaTAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAacac > 1:1193227/1‑76 (MQ=255)
aTAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAacaca > 2:538427/1‑76 (MQ=255)
aaaCTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACg > 2:608564/1‑76 (MQ=255)
aaaCTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACg > 1:1879489/1‑76 (MQ=255)
aaCTTCTTCTTCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGc < 1:700914/76‑1 (MQ=255)
cttcttcttCGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCtg < 2:1481186/76‑1 (MQ=255)
tcttcttcGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCtgtg > 1:548772/1‑76 (MQ=255)
tcttcttcGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCtgtg > 1:504043/1‑76 (MQ=255)
ttcttcGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCtgtgtg < 2:1076524/76‑1 (MQ=255)
ttcttcGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCtgtgtg < 1:520363/76‑1 (MQ=255)
ttcGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCt < 2:1388414/76‑1 (MQ=255)
tcGGCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGCGTGGCTc > 2:652942/1‑76 (MQ=255)
gCCGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCt < 2:462634/76‑1 (MQ=255)
cGTTAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGc > 2:257258/1‑76 (MQ=255)
ttAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGa > 1:413118/1‑76 (MQ=255)
ttAACAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGa > 2:1270526/1‑76 (MQ=255)
aaCAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATa > 2:1842661/1‑76 (MQ=255)
aaCAGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATa > 1:681399/1‑76 (MQ=255)
aGTGGTGAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACa > 1:1198893/1‑76 (MQ=255)
gtggtgAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAg > 1:15414/1‑76 (MQ=255)
tggtgAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGt > 2:1952920/1‑76 (MQ=255)
gtgAATGACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTc > 2:490740/1‑76 (MQ=255)
|
CGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTC > REL606/2762141‑2762283
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
