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 |
|
A11 F1 I1 R1
|
63 |
64.8 |
2934156 |
93.7% |
2749304 |
111.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,594,256 |
(C)8→9 |
pseudogene (3732/3861 nt) |
yneO ← |
pseudogene, AidA homolog |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,594,248 | 1 | . | C | 89.8%
| 198.6
/ 13.4
| 59 | pseudogene (3740/3861 nt) | yneO | pseudogene, AidA homolog |
| Reads supporting (aligned to +/- strand): ref base . (2/4); new base C (27/26); total (29/30) |
| Fisher's exact test for biased strand distribution p-value = 6.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01 |
AGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAG > NC_000913/1594111‑1594377
|
aGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑cc > 2:1133228/1‑139 (MQ=255)
acacGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑cccccc > 2:491539/1‑139 (MQ=255)
cccccccAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGatat < 2:417699/139‑1 (MQ=255)
ccccAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCATACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCcg < 1:207550/139‑1 (MQ=255)
ccccAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCcg > 1:403545/1‑139 (MQ=255)
aaCGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTg > 1:171891/1‑139 (MQ=255)
ccTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGaa < 1:939288/139‑1 (MQ=255)
ccTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGaa > 2:592369/1‑138 (MQ=255)
ccTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGaa < 1:592369/138‑1 (MQ=255)
tGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATc < 1:491539/139‑1 (MQ=255)
tGCAGTGGTGACATTTCCCGACATCACACCGCTGTCATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATc < 1:13691/139‑1 (MQ=255)
cAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCgt < 2:403545/139‑1 (MQ=255)
gACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAag < 1:670478/139‑1 (MQ=255)
tCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGaa < 2:757193/122‑1 (MQ=255)
tCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGaa > 1:757193/1‑122 (MQ=255)
tCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAg < 2:956418/139‑1 (MQ=255)
aCATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATcc < 1:311762/139‑1 (MQ=255)
cacaCCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑cccc > 2:953600/1‑75 (MQ=255)
cacaCCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑cccc < 1:953600/75‑1 (MQ=255)
cacCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTAc > 2:830646/1‑139 (MQ=255)
cTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGt > 1:613974/1‑139 (MQ=255)
tGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGtt > 1:702762/1‑139 (MQ=255)
tttttggtttttaTGTGTTTACTTTCCATTTTAATGGCCAGATTCGAACCCGAAACAAATTCCC‑‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGtt < 2:1258536/127‑1 (MQ=255)
ttATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑cccccc > 1:1284754/1‑67 (MQ=255)
ttATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑cccccc < 2:1284754/67‑1 (MQ=255)
tatTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCa < 2:773589/126‑1 (MQ=255)
tatTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCa > 1:773589/1‑126 (MQ=255)
atTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATc > 1:716417/1‑139 (MQ=255)
tAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATAcg < 2:1427736/85‑1 (MQ=255)
tAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATAcg > 1:1427736/1‑85 (MQ=255)
tgtgTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGat < 2:519388/62‑1 (MQ=255)
tgtgTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGat > 1:519388/1‑62 (MQ=255)
tgtgTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgc > 1:805321/1‑139 (MQ=255)
gtgtTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct < 2:613974/139‑1 (MQ=255)
gtTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATTCGTCGTACCCTGATACGCCGCGGAATCgttgtt > 1:1078268/1‑95 (MQ=255)
gtTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 1:369951/139‑1 (MQ=255)
gtTGACTTGCCATATTAAGGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑CCCCCCCGCACGATATTCGTCGTACCCTGATACGCCGCGGAATCgttgtt < 2:1078268/95‑1 (MQ=255)
ttGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTa < 2:336807/95‑1 (MQ=255)
ttGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTa > 1:336807/1‑95 (MQ=255)
gCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGaa > 1:201477/1‑79 (MQ=255)
gCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGaa < 2:201477/79‑1 (MQ=255)
ccATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt > 1:1416809/1‑86 (MQ=255)
ccATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt < 2:1416809/86‑1 (MQ=255)
ccATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac > 2:822838/1‑130 (MQ=255)
ccATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 1:822838/130‑1 (MQ=255)
atatTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACtg > 1:1415031/1‑139 (MQ=255)
atTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGTTACCCAGTTTTGTCACATCACCGCTACCGCTGATACtgtg < 1:1174182/139‑1 (MQ=255)
aTGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt > 2:884038/1‑78 (MQ=255)
aTGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt < 1:884038/78‑1 (MQ=255)
tGG‑CAGAGTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCa > 2:1139243/1‑139 (MQ=255)
agTCGGAACCGCAAGCAATT‑‑TC‑CCCCCCC‑CAGGCAATCCGCCGTACCCTGATACGCCGAGGAAGCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCCTCATCGccc > 2:133756/1‑139 (MQ=255)
agTCGGAACCGAAAGCAATT‑‑TCCCCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc > 2:1083807/1‑139 (MQ=255)
agTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAaga > 1:407139/1‑75 (MQ=255)
agTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAaga < 2:407139/75‑1 (MQ=255)
agTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTAcc > 1:203125/1‑92 (MQ=255)
agTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTAcc < 2:203125/92‑1 (MQ=255)
agTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTc < 2:702471/132‑1 (MQ=255)
agTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTc > 1:702471/1‑132 (MQ=255)
agTCGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGccc > 2:1289977/1‑139 (MQ=255)
cGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 2:526401/112‑1 (MQ=255)
cGGAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac > 1:526401/1‑112 (MQ=255)
gAACCGAAAGCAATT‑‑TCCCCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCt < 1:1083807/139‑1 (MQ=255)
gAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 1:1125143/110‑1 (MQ=255)
gAACCGAAAGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac > 2:1125143/1‑110 (MQ=255)
aaGCAATT‑‑TC‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAg > 2:153115/1‑139 (MQ=255)
|
AGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGG‑CAGAGTCGGAACCGAAAGCAATT‑‑T‑‑CCCCCCC‑CACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAG > NC_000913/1594111‑1594377
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
