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 F169 I0 R1
|
75 |
34.0 |
794130 |
95.7% |
759982 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,709,439 |
Δ1 bp |
100% |
coding (1488/1812 nt) |
oatA_2 ← |
O‑acetyltransferase OatA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,709,439 | 0 | T | . | 83.3%
| 67.0
/ 12.7
| 24 | coding (1488/1812 nt) | oatA_2 | O‑acetyltransferase OatA |
| Reads supporting (aligned to +/- strand): ref base T (4/0); new base . (8/12); total (12/12) |
| Fisher's exact test for biased strand distribution p-value = 9.32e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCA > USA300TCH1516_ALE/2709306‑2709574
|
tACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCtttttagc < 2:230193/141‑4 (MQ=255)
ccTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACTTTTTTTAGCa > 1:347495/1‑141 (MQ=255)
cATAATCTCTAGGTACTCTAATAGAAACTAAATATCTGTCTGCTTTTCCAAAACTATCCATTAGTTCATTTAGTTGATCTTTCGTAAATGCCCCATTTGTACTCAGCTCTACTACACCTTTTTGACC‑TTTTTAGCATattt > 2:43016/1‑138 (MQ=255)
aTAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCt > 2:262848/1‑141 (MQ=255)
gTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCAGAGTCTTTATATTGCGa > 2:308405/1‑141 (MQ=255)
atatGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATc < 1:296663/141‑1 (MQ=255)
atGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCaa < 1:194688/141‑1 (MQ=255)
ttcccAAAACTATCCAATAGTTCATTTAATTGAACTTTCGTAAATGCCCCAATTGTCCCAAGCACTACTACAACTTTTTGACCTTTCTTAGCATAGTCGTTATATTGCGATTTCACACTTGTTATAACATCAACGAGTTGc > 2:356824/4‑141 (MQ=255)
ccAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTGCTACAACTTTTCGACC‑TTTTTAGCATAGTCTTTATATTGCAATTTCACAATTGGTGTTGCATCAACGAGTTGCCGTc > 1:12173/1‑141 (MQ=255)
aCTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACt > 2:243319/1‑141 (MQ=255)
cAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCa < 2:337407/141‑1 (MQ=255)
aaTTGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCAt < 2:361685/141‑1 (MQ=255)
aaTAGTTCATTTAATTGATCTTTCGTAAATGCCTCATTTGTACCAAGCTCTACGAGAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTGCACAATTGGTGTAGCATCAACGACTTGCCGTCCAACTTTACCAt < 2:216360/141‑1 (MQ=255)
aTAGTTCATTTAATTGAGCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATc < 1:48948/141‑1 (MQ=255)
tttAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTtgtg < 2:302087/141‑1 (MQ=255)
tGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGCTTTCACAAGTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTg < 2:163202/141‑1 (MQ=255)
aTCTTTCGTAAATGCCCCATGTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTGTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGt > 1:256193/1‑141 (MQ=255)
tCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTTCATTTGGTAttt > 2:350020/1‑141 (MQ=255)
tCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTAttt > 2:350009/1‑141 (MQ=255)
tAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTTTAGCATCAACGAGTTGCCGTCAAACTTTACCATCCATTTGTGCATTTGGTATTTTCtt > 2:177591/1‑141 (MQ=255)
tGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTa < 1:377651/141‑1 (MQ=255)
ccAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCaa > 1:190655/1‑141 (MQ=255)
cAACTTTTTGACC‑CTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGAc < 1:6591/141‑1 (MQ=255)
aaCTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGAcc < 1:15590/141‑1 (MQ=255)
ttGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCa < 1:262848/141‑1 (MQ=255)
|
TACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCA > USA300TCH1516_ALE/2709306‑2709574
|
| 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
