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 |
|
A2 F999 I1 R1
|
226 |
132.7 |
9745491 |
85.7% |
8351885 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,944,676 |
2 bp→GC |
intergenic (+20/+75) |
trpT → / ← yifDA |
tRNA‑Trp/transcription regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,944,676 | 0 | C | G | 98.6%
| 185.4
/ ‑3.9
| 71 | intergenic (+20/+76) | trpT/yifDA | tRNA‑Trp/transcription regulator |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base G (25/45); total (25/46) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
| * | NC_000913 | 3,944,677 | 0 | G | C | 98.6%
| 181.5
/ ‑4.9
| 71 | intergenic (+21/+75) | trpT/yifDA | tRNA‑Trp/transcription regulator |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (25/45); total (25/46) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
GGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAACG‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAT > NC_000913/3944609‑3944746
||
ggTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAt < 1:741283/76‑1 (MQ=255)
ggTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAt > 1:780127/1‑76 (MQ=255)
ggTCTCCAAAACCGGGAGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAt > 2:1794386/1‑76 (MQ=255)
gTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAtt < 2:2715200/76‑1 (MQ=255)
tctcCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAttt < 2:2541967/76‑1 (MQ=255)
tctcCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCCGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGActt > 2:3227477/1‑76 (MQ=255)
ctcCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAtttt < 1:4739569/76‑1 (MQ=255)
ctcCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAtttt > 2:4399363/1‑76 (MQ=255)
ccAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAtttttt > 1:2357259/1‑76 (MQ=255)
cAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAttttttt < 1:4740084/76‑1 (MQ=255)
aaaaCCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGAtttttttt < 2:847063/76‑1 (MQ=255)
aaaCCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTa < 1:3233413/76‑1 (MQ=255)
aaaCCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAACCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTa < 2:4076399/76‑1 (MQ=255)
aaCCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTAt > 1:265195/1‑76 (MQ=255)
acggggTGTTGTGATTTCGAGTCGCTCGCCCCCTGCCAGAAATCATCCTTAGC‑TAACGCTAATGATTTTTTTtctc < 2:1313379/73‑1 (MQ=255)
ccGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCt < 2:1464688/76‑1 (MQ=255)
gggTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTCTCTGa > 2:861941/1‑76 (MQ=255)
gggTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGa > 2:955288/1‑76 (MQ=255)
ggTGTTGGGGGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGaa < 2:4380402/76‑1 (MQ=255)
ggTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGaa < 2:2094430/76‑1 (MQ=255)
ggTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGaa < 2:4366122/76‑1 (MQ=255)
gtgtTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGaaa < 2:3938300/76‑1 (MQ=255)
gtgtTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGaaa > 2:2333925/1‑76 (MQ=255)
gtTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGACATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATa < 1:3036523/76‑1 (MQ=255)
gtTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTCTCTGAAATa > 1:4789725/1‑76 (MQ=255)
ttGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATaa < 2:3939198/76‑1 (MQ=255)
gggAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAAcc > 2:1748506/1‑76 (MQ=255)
ggAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAAccc < 1:3990733/76‑1 (MQ=255)
gAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCct < 1:2673447/76‑1 (MQ=255)
aGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCctc < 2:1406732/76‑1 (MQ=255)
aGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCctc > 2:4782054/1‑76 (MQ=255)
gTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCctct < 2:2056307/76‑1 (MQ=255)
tgcGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCtctc < 1:1795322/74‑1 (MQ=255)
tCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTcc > 2:4213641/1‑76 (MQ=255)
tCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTcc < 2:2215950/76‑1 (MQ=255)
tCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTcc < 2:3639685/76‑1 (MQ=255)
tCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTcc < 1:244475/76‑1 (MQ=255)
tCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTcc < 1:451971/76‑1 (MQ=255)
ggAGTCGCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCg < 2:1528386/75‑1 (MQ=255)
cGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCg < 2:606002/76‑1 (MQ=255)
aGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGaa > 2:1613907/1‑76 (MQ=255)
aGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGaa < 1:3476808/76‑1 (MQ=255)
ttctctcCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAg > 2:2858069/2‑76 (MQ=255)
gTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAg < 2:1291432/76‑1 (MQ=255)
gTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAg < 2:3019197/76‑1 (MQ=255)
tctcCGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTaa < 1:275402/76‑1 (MQ=255)
cccGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAAt < 2:524560/75‑1 (MQ=255)
ccGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATc > 1:2268625/1‑76 (MQ=255)
ccGCCCCTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATc < 1:980655/76‑1 (MQ=255)
ccccTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCtt > 2:4348947/1‑76 (MQ=255)
cccTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTc > 2:1844549/1‑76 (MQ=255)
cccTGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTc < 2:4056008/76‑1 (MQ=255)
tGCCAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTAc < 2:1182333/76‑1 (MQ=255)
ccAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCg > 1:2796889/1‑76 (MQ=255)
ccAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCg > 2:4404019/1‑76 (MQ=255)
cAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCgg > 2:2701762/1‑76 (MQ=255)
cAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCgg < 1:3580248/76‑1 (MQ=255)
cAGAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCgg < 1:869652/76‑1 (MQ=255)
gAAATCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCa < 2:780127/76‑1 (MQ=255)
aaaTCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCAt > 2:3615819/1‑76 (MQ=255)
aaTCATCCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCAGAAGTAAATCCTTCTACCGGCATc > 1:4797634/1‑76 (MQ=255)
taatcCTAGGCGAAAGC‑TAGGGTTTTTTTTAATCGGAAATAACCCTCCCCGAATT‑AATCCTTCTACCGGCATCCtt < 2:3794749/74‑1 (MQ=255)
catcCTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCtt > 2:2144199/1‑76 (MQ=255)
ccTTAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgcc < 1:3554265/76‑1 (MQ=255)
ttAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgccga < 1:4399363/76‑3 (MQ=255)
ttAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgccag < 1:2404261/76‑1 (MQ=255)
tAGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgccagc < 1:2478929/76‑1 (MQ=255)
aGCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgccagcc > 1:3552124/1‑76 (MQ=255)
gCGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgccagcca < 2:445702/76‑1 (MQ=255)
cGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAt < 2:4423405/76‑1 (MQ=255)
cGAAAGC‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAt < 2:288345/76‑1 (MQ=255)
||
GGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAACG‑TAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAT > NC_000913/3944609‑3944746
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
