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 I1 R1
|
62 |
44.4 |
970160 |
98.1% |
951726 |
147.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,709,444 |
(T)6→5 |
coding (1483/1812 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 | . | 93.3%
| 178.5
/ 5.7
| 45 | coding (1488/1812 nt) | oatA_2 | O‑acetyltransferase OatA |
| Reads supporting (aligned to +/- strand): ref base T (3/0); new base . (20/22); total (23/22) |
| Fisher's exact test for biased strand distribution p-value = 2.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTATTCTACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATT > USA300TCH1516_ALE/2709300‑2709580
|
ttattCTACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCtttttagca < 3:273353/148‑5 (MQ=255)
ttattCTACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCtttttagca < 4:110034/148‑5 (MQ=255)
ttattCTACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCtttttagca > 4:220306/1‑144 (MQ=255)
ttattCTACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCtttttagca > 3:227212/1‑144 (MQ=255)
aCCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCtt < 4:170479/148‑1 (MQ=255)
aCCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCtt < 3:49735/148‑1 (MQ=255)
tCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTtata > 3:403335/1‑148 (MQ=255)
tCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTtata > 3:380316/1‑148 (MQ=255)
tCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTtata > 4:345439/1‑148 (MQ=255)
tCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTG‑TCTTTTTTAGCATAGTCTTtata > 4:1645/1‑148 (MQ=255)
tCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGGCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCTAATTTGTACCAAACTCTACTACAACTTTTTGACC‑CTTTTAGCATAGTCTTtata > 4:368857/1‑148 (MQ=255)
tAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTc < 4:125335/148‑1 (MQ=255)
tAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTc < 4:31944/148‑1 (MQ=255)
aTAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACaa > 1:38915/1‑141 (MQ=255)
aaTATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGc < 2:27743/141‑1 (MQ=255)
atatGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGt > 4:335318/1‑148 (MQ=255)
tGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGc > 3:393280/1‑148 (MQ=255)
tGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGATC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTc > 4:118912/1‑148 (MQ=255)
tGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTc < 3:285000/148‑1 (MQ=255)
tGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTc < 4:221784/148‑1 (MQ=255)
ttttCCAAATCTATCCAATAGTTCATTTAATTTATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTGGTCC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCaa < 4:373206/148‑1 (MQ=255)
ttttCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGc > 2:15191/1‑141 (MQ=255)
ttCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCg < 2:32451/141‑1 (MQ=255)
cAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAttt < 3:167179/148‑1 (MQ=255)
aTAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTtgt < 4:412880/148‑1 (MQ=255)
cATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCAttt > 3:202649/1‑148 (MQ=255)
cATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTT‑TTCTTTTTTTTCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCAttt > 4:228576/1‑148 (MQ=255)
tttAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTgg > 4:157233/1‑148 (MQ=255)
gATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTgg > 2:42661/1‑141 (MQ=255)
gATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTc < 4:54826/148‑1 (MQ=255)
cTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTa > 3:6223/1‑148 (MQ=255)
cTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTa > 3:63191/1‑148 (MQ=255)
cTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTa < 3:305444/148‑1 (MQ=255)
ttCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGt < 4:408983/148‑1 (MQ=255)
ttCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGCAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGt < 3:211919/148‑1 (MQ=255)
ttCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATCTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGt < 3:25699/148‑1 (MQ=255)
cGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTc < 1:23077/141‑1 (MQ=255)
cGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTaa < 3:89913/148‑1 (MQ=255)
tAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAg < 4:404420/148‑1 (MQ=255)
aaaTGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGa > 4:201659/1‑148 (MQ=255)
aaaTGCCCCATTTGTACCAAGCCCTACTACAACTTTTTGACC‑TCTTTAGCATAGTCTTTATATTGCGATGTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTCAGTAAAGa > 4:136974/1‑148 (MQ=255)
gCCCCATTTGTACCAACCCCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCCTCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACAtt < 3:335318/148‑1 (MQ=255)
ccATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGa > 1:34750/1‑141 (MQ=255)
aCCAAGCTCTACTACAACTTTTT‑TTTTTTTTTTTCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGTTATTTTCTTAGTAAAGACATTACCAATATcca > 4:236996/1‑148 (MQ=255)
ccAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATccac > 3:302569/1‑148 (MQ=255)
aGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACTTTACCAACATCCACCAt > 4:3086/1‑148 (MQ=255)
acAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTc < 3:180279/148‑1 (MQ=255)
cAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGAc < 1:15191/141‑1 (MQ=255)
tttGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAAtt > 3:402263/1‑148 (MQ=255)
|
TTATTCTACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATT > USA300TCH1516_ALE/2709300‑2709580
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
