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 |
|
A4 F1 I1 R1
|
765 |
39.6 |
1867486 |
94.4% |
1762906 |
108.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,475,562 |
(G)6→7 |
coding (126/1815 nt) |
yjgL → |
SopA‑central‑domain‑like hexapeptide repeat protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,475,556 | 1 | . | G | 97.1%
| 121.7
/ ‑3.6
| 35 | coding (120/1815 nt) | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (18/16); total (19/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑GGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCAT > NC_000913/4475423‑4475688
|
tCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggg > 2:826338/1‑139 (MQ=255)
tCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggg > 1:502756/1‑139 (MQ=255)
aaGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg < 2:629186/139‑2 (MQ=255)
aaGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg < 2:276823/139‑2 (MQ=255)
aaGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg < 1:767589/139‑2 (MQ=255)
gTTCGTCATGAGCAAAATATCAGATTTAAATTATGCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGGGAAGATTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGa < 2:888870/139‑1 (MQ=255)
cGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATaa > 2:576476/1‑139 (MQ=255)
gAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAg < 1:579038/139‑1 (MQ=255)
aaTATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAatat > 1:572561/1‑139 (MQ=255)
aaTATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAatat > 1:593658/1‑139 (MQ=255)
ttCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATCAATGCTTTTGCCCGTATTGCTG‑GGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCAtt > 2:222871/1‑139 (MQ=255)
aaCACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTag > 2:847641/1‑139 (MQ=255)
attacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAg > 1:425587/1‑125 (MQ=255)
attacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAg < 2:425587/125‑1 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATa > 2:170617/1‑96 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATa < 1:170617/96‑1 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAg < 1:250952/100‑1 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAg > 2:250952/1‑100 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGttttt > 1:831303/1‑139 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg > 2:373310/1‑88 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg < 1:373310/89‑2 (MQ=255)
taGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaa > 1:801747/1‑139 (MQ=255)
aGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaaa < 1:67410/139‑1 (MQ=255)
gCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg > 2:568871/1‑81 (MQ=255)
gCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg < 1:568871/82‑2 (MQ=255)
aCAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGatat < 2:831303/139‑1 (MQ=255)
cAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGatat > 2:729240/1‑138 (MQ=255)
cAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGatat < 1:729240/138‑1 (MQ=255)
ttAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTAccc < 2:801747/139‑1 (MQ=255)
aCAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTggg < 1:788171/139‑1 (MQ=255)
aCAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTggg > 2:339563/1‑139 (MQ=255)
cTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGatat > 2:353538/1‑105 (MQ=255)
cTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGatat < 1:353538/105‑1 (MQ=255)
ggCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCa > 2:293968/1‑139 (MQ=255)
ggCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg > 1:110762/1‑41 (MQ=255)
ggCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑ggggggg < 2:110762/42‑2 (MQ=255)
cGTGTTGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAAc > 2:453390/1‑139 (MQ=255)
cGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑gggggggc > 2:775723/1‑39 (MQ=255)
cGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑gggggggc < 1:775723/41‑3 (MQ=255)
ttGGAATGAATGATTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAg > 1:862176/1‑139 (MQ=255)
gaatgaTTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAg < 1:861504/139‑1 (MQ=255)
aatgaTTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCa > 1:87977/1‑82 (MQ=255)
aatgaTTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCa < 2:87977/82‑1 (MQ=255)
aatgaTTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGa > 1:432868/1‑108 (MQ=255)
aatgaTTTTGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGa < 2:432868/108‑1 (MQ=255)
tGCCCGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATatgat < 1:453390/139‑1 (MQ=255)
cGTATTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCt < 2:502756/139‑1 (MQ=255)
aTTGC‑CGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCat > 2:885869/1‑139 (MQ=255)
|
TCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGC‑C‑GGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCAT > NC_000913/4475423‑4475688
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
