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 |
|
A3 F1 I1 R1
|
781 |
46.9 |
2231650 |
93.5% |
2086592 |
109.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,973,410 |
A→G |
G151G (GGT→GGC) |
lplT ← |
lysophospholipid transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,973,410 | 0 | A | G | 95.8%
| 155.7
/ ‑2.4
| 48 | G151G (GGT→GGC) | lplT | lysophospholipid transporter |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (24/22); total (25/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.18e-01 |
AGGACTGCCCCGGACGCGCCGCCGCCAGTTTGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCGTATTTCGCCGGTGAATAGGCTGCAGCACCAACACCCAC > NC_000913/2973277‑2973538
|
aGGACTGCCCCGGACGCGCCGCCGCCAGTTTGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAg > 1:10223/1‑139 (MQ=255)
gCCCCGGACGCGCCGCCGCCAGTTTGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAAt < 1:644867/139‑1 (MQ=255)
gccgccgccAGTTTGGGAATGTGGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATgg > 2:544046/1‑139 (MQ=255)
gccgccgccAGTTTGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATgg > 2:814600/1‑139 (MQ=255)
ccgccgccAGTTTGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGt > 1:803159/1‑139 (MQ=255)
cAGTTTGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCt < 1:814600/139‑1 (MQ=255)
tAGGTATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCACCGCt > 2:715297/1‑114 (MQ=255)
tAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCACCGCt < 1:715297/114‑1 (MQ=255)
atTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCt < 1:544046/139‑1 (MQ=255)
atTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCt < 2:803159/139‑1 (MQ=255)
gCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCa > 1:67834/1‑139 (MQ=255)
cAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCAc > 2:335438/1‑139 (MQ=255)
cAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCAc < 2:265783/139‑1 (MQ=255)
aaCGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACt < 2:577947/139‑1 (MQ=255)
aaCGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACt < 2:67834/139‑1 (MQ=255)
aCGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTa > 2:830661/1‑139 (MQ=255)
aCCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATcgccgc > 2:921431/1‑98 (MQ=255)
aCCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATcgccgc < 1:921431/98‑1 (MQ=255)
caccacCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGTCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCa < 2:685539/129‑1 (MQ=255)
caccacCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGACGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCa > 1:685539/1‑129 (MQ=255)
ccGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCg > 1:436531/1‑139 (MQ=255)
gCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTa > 2:804872/1‑139 (MQ=255)
gTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCtt > 2:342342/1‑93 (MQ=255)
gTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCtt < 1:342342/93‑1 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCg > 1:293300/1‑139 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCg > 2:290610/1‑139 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCg > 1:712524/1‑139 (MQ=255)
cgcATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATcgc < 1:667935/73‑1 (MQ=255)
cacATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATcgc > 2:667935/3‑73 (MQ=255)
tGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCgaga < 2:343080/139‑1 (MQ=255)
ggCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATa < 2:293300/139‑1 (MQ=255)
gaGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCGTATTTCGcc < 2:997227/139‑1 (MQ=255)
cATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAg < 1:494590/81‑1 (MQ=255)
cATGCCAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAg > 2:494590/1‑81 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTaa > 2:264136/1‑87 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTaa < 1:264136/87‑1 (MQ=255)
aGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGcc < 2:16659/109‑1 (MQ=255)
aGTCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGcc > 1:16659/1‑109 (MQ=255)
tCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCtt < 2:328732/58‑1 (MQ=255)
tCAGCCAGCACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCtt > 1:328732/1‑58 (MQ=255)
gccagcACACCACCGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCGTATTTCGCCGGTGAATAGGCTgcag > 1:859100/1‑139 (MQ=255)
ccaccGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCg > 2:77542/1‑105 (MQ=255)
ccaccGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCg < 1:77542/105‑1 (MQ=255)
caccGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCGTATTTCGCCGGTGAATAGGCTGCAGCAc > 2:276667/1‑132 (MQ=255)
caccGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCGTATTTCGCCGGTGAATAGGCTGCAGCAc < 1:276667/132‑1 (MQ=255)
accGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAg < 2:371464/38‑1 (MQ=255)
accGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAg > 1:371464/1‑38 (MQ=255)
cGGCTACGGAGCCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCGTATTTCGCCGGTGAATAGGCTGCAGCACCAAcacccac < 2:10223/139‑1 (MQ=255)
|
AGGACTGCCCCGGACGCGCCGCCGCCAGTTTGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTTACTACCCGTGGTTAATTCGCCGAGAATACCGTATTTCGCCGGTGAATAGGCTGCAGCACCAACACCCAC > NC_000913/2973277‑2973538
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
