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 F71 I1 R1
|
31 |
24.1 |
564604 |
94.3% |
532421 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,224,476 |
T→C |
P233P (CCA→CCG) |
atpA ← |
ATP synthase subunit alpha |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,224,476 | 0 | T | C | 95.8%
| 73.3
/ NA
| 24 | P233P (CCA→CCG) | atpA | ATP synthase subunit alpha |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (17/6); minor base G (1/0); total (18/6) |
| 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 |
ACTCACGATAAGCTGCTGCTTGTTTAGTTAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAATGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATTTGCTCTTACTGTTGAATCTTTTTGACCAATAGCAACATAGATACAAATCGTACCTTG > USA300TCH1516_ALE/2224358‑2224610
|
aCTCACGATAAGCTGCTGCTTGTTTAGTTAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGAtg > 1:5750/1‑141 (MQ=255)
aaGCTGCTGCTTGTGTAGTTAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTacaa > 2:217618/1‑141 (MQ=255)
gctgctgctTGTTTAGTTAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTacaaca > 1:112932/1‑141 (MQ=255)
tgctgctTGTTTAGTTAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAAt < 1:251846/141‑1 (MQ=255)
gTTTAGTTAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGt < 2:41477/141‑1 (MQ=255)
tAGTTAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTa > 1:202988/1‑141 (MQ=255)
tAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGGGTAGTCTAAAgc > 1:152713/1‑141 (MQ=255)
atcatcATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTAAAACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGcc > 2:155948/1‑141 (MQ=255)
atcatcATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCAATTGTTTCACCTGAATATGGTGCAATATATAATAACGGATAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGcc > 2:187344/1‑141 (MQ=255)
atcatAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGc < 1:235993/141‑1 (MQ=255)
aaaCGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTc > 2:219198/1‑141 (MQ=255)
cATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCaa < 1:322/141‑1 (MQ=255)
ttACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACAttt > 1:159569/1‑141 (MQ=255)
aTGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATTTGCTCTTACTGtt > 1:255989/1‑141 (MQ=255)
tGAATTCTTCACCCATTTTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTTCTTGTCTTAACTTTTCAACATTTGCTCTTACTGTTg < 1:164808/141‑1 (MQ=255)
ttcttcACCCATTGTTACACCTGAATATGGTGCAATATATAATAAGGGAGAAGGTTCAGAAGCTGATCATGATATGGCAATAGTGTAGTCTAAAGCGCCTGCATGTCTTAACTTTTCAACATTTGCTTTTACTGTTGAATc > 1:279832/1‑141 (MQ=255)
ttcttcACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACCTTTGCTCTTACTCTTGAATc > 2:94522/1‑141 (MQ=255)
tcACCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATTTGCTCTTACTGTTGAATCtttt > 1:211854/1‑141 (MQ=255)
aCCCATTGTTACACCTGAATATGGTGCAATATATAATAACGGAGAAAGTTCAAAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATCAACGCGAACCTTTGAATCtttttt > 2:15619/1‑140 (MQ=255)
aaTATGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATTTGCTCTTACTGTTGAATCTTTTTGACCAATAGCAACATAGa > 2:233136/1‑141 (MQ=255)
atatGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATTTGCTCTTACTGTTGAATCTTTTTGACCAATAGCAACATAGAt > 2:11386/1‑141 (MQ=255)
tGGTGCAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTACCTTTTCAACATTTGCTCTTCCTGTTGAATCTTTTTGACCAATAGCAACATAGATACa > 2:59884/1‑141 (MQ=255)
cAATATATAATAACGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATTTGCTCTTACTGTTGAATCTTTTTGACCAATAGCAACATAGATACAAATCg > 2:80730/1‑141 (MQ=255)
taataaCGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATTTGCTCTTACTGTTGAATCTTTTTGACCAATAGCAACATAGATACAAATCGTACCTTg < 1:70428/141‑1 (MQ=255)
|
ACTCACGATAAGCTGCTGCTTGTTTAGTTAAATCATCATAAACGATTAAAACATGTTTACCGTTAAACATGAATTCTTCACCCATTGTTACACCTGAATATGGTGCAATATATAATAATGGAGAAGGTTCAGAAGCTGATGCTGCTACAACAATAGTGTAGTCTAAAGCGCCTGCTTGTCTTAACTTTTCAACATTTGCTCTTACTGTTGAATCTTTTTGACCAATAGCAACATAGATACAAATCGTACCTTG > USA300TCH1516_ALE/2224358‑2224610
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
