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 F1 I1 R1
|
1548 |
369.5 |
20095359 |
96.9% |
19472402 |
93.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,096,260 |
(G)7→8 |
intergenic (+208/+528) |
ycdU → / ← serX |
hypothetical protein/tRNA‑Ser |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,096,253 | 1 | . | G | 81.2%
| 32.5
/ 4.9
| 16 | intergenic (+201/+535) | ycdU/serX | hypothetical protein/tRNA‑Ser |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base G (1/12); total (3/13) |
| Fisher's exact test for biased strand distribution p-value = 7.14e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑GGGGGGG‑ATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACC > NC_000913/1096161‑1096342
|
ccTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTGCTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGa < 1:8709591/93‑1 (MQ=255)
ccTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGa < 1:2096765/93‑1 (MQ=255)
ccTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGa < 2:2546104/93‑1 (MQ=255)
cTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACGAAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGa < 1:9639268/93‑1 (MQ=255)
cTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑g < 1:3216720/93‑1 (MQ=255)
cTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑g < 1:7223364/93‑1 (MQ=255)
cTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑g < 2:5483123/93‑1 (MQ=255)
cTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGA‑‑g > 1:2309402/1‑93 (MQ=255)
tAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gg < 1:2671470/93‑1 (MQ=255)
tAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gg < 2:5871184/93‑1 (MQ=255)
tAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gg < 1:4572452/93‑1 (MQ=255)
tAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gg > 1:57454/1‑93 (MQ=255)
aCAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gggg < 1:8430028/93‑1 (MQ=255)
aCAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gggg < 2:535473/93‑1 (MQ=255)
aCAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑‑AAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggg < 2:5444386/93‑1 (MQ=255)
cAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggg < 2:314503/93‑1 (MQ=255)
aggcGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gggggg < 2:2779483/90‑1 (MQ=255)
aGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gggggg > 1:6689250/1‑93 (MQ=255)
aGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gggggg < 1:4521865/93‑1 (MQ=255)
aGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGCGT‑‑gggggg > 2:336568/1‑93 (MQ=255)
aGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAACATGGCGGTGA‑‑gggggg < 2:6705960/93‑1 (MQ=255)
gccGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggg < 2:3235483/91‑1 (MQ=255)
gACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggg < 1:6879877/93‑1 (MQ=255)
gACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggg > 2:6098998/1‑93 (MQ=255)
gACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggg > 2:6098999/1‑93 (MQ=255)
gACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggg < 2:7695334/93‑1 (MQ=255)
gACGTGGGCGGGGGCACCCGGTGTGAGCAATAAACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGACGGTGA‑‑ggggggg < 2:8920497/93‑1 (MQ=255)
aCGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gggggggg < 2:5521488/93‑2 (MQ=255)
aCGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gggggggg < 2:2401600/93‑2 (MQ=255)
cGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑gggggggga < 2:9845604/93‑3 (MQ=255)
cGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGA‑‑gggggggga > 1:4279831/1‑91 (MQ=255)
gTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggggat < 1:7624613/93‑4 (MQ=255)
gTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggggat < 1:6155616/93‑4 (MQ=255)
gTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggggat < 1:5887407/93‑4 (MQ=255)
gTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggggat < 2:2561061/93‑4 (MQ=255)
tGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggggggg > 2:199847/1‑89 (MQ=255)
tGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑ggggggggatt > 1:10016457/1‑89 (MQ=255)
tGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑GGGGGGG‑GTTg > 2:2494313/1‑93 (MQ=255)
tGGGCGGGGGCACCCGGGGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTCAATATGGCGGTGC‑‑ggggggggggt > 1:3033952/1‑89 (MQ=14)
ggggggggCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGa < 1:7431761/90‑1 (MQ=255)
ggCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGa < 1:6256818/93‑1 (MQ=255)
gCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGAc < 1:1551715/93‑1 (MQ=255)
gCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑GGGGGGGTATTGAc < 2:9758054/93‑1 (MQ=255)
cGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCCTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGAcc > 2:293533/1‑92 (MQ=14)
gggggCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtc < 2:503447/93‑1 (MQ=255)
gggggCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtc < 1:7652252/93‑1 (MQ=255)
gggggCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtc < 1:6155017/93‑1 (MQ=255)
gggggCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtc < 2:7947180/93‑1 (MQ=255)
ggggCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtcg > 2:8487229/1‑93 (MQ=255)
ggCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtcgct < 1:6189557/93‑1 (MQ=255)
gCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtcgctt < 2:138261/93‑1 (MQ=16)
cACCGGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtcgcttc < 2:3987762/93‑1 (MQ=255)
cACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGG‑ATTGACtcgctt < 1:4858880/93‑1 (MQ=11)
cACCCGGTGTCTACAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAG‑GGGGGGG‑ATTGACtcgcttc < 2:7234381/93‑1 (MQ=11)
gTGA‑‑GGGGGGG‑ATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCCCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCCGTTGTCggac > 2:6133227/1‑90 (MQ=0)
|
CCTAACAGACGTGGGCGGGGGCACCCGGTGTGTGCAATATACG‑AAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑‑GGGGGGG‑ATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACC > NC_000913/1096161‑1096342
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
