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 |
2,314,956 |
+C |
coding (1469/2673 nt) |
rcsD → |
phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,314,952 | 1 | . | C | 94.1%
| 109.6
/ 0.2
| 34 | coding (1465/2673 nt) | rcsD | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (16/16); total (17/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.89e-01 |
CAAGAAACTCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACG‑C‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTGAGACGGTGCTGTTCTCCGTGCAGGATTT > NC_000913/2314822‑2315082
|
cAAGAAACTCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACG‑c‑ccccgga < 1:369015/139‑5 (MQ=255)
aaCTCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCa > 2:697599/1‑139 (MQ=255)
aatCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTCATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACGGTCCCGGGCGGAGAGAACGGCTAAAATCAACG‑CGCCCGGAAAGCaa > 2:700106/3‑139 (MQ=255)
tCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAaac < 1:39359/139‑1 (MQ=255)
gCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCa < 1:20989/139‑1 (MQ=255)
aCCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGc > 2:1020690/1‑139 (MQ=255)
ccAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCg < 1:697599/139‑1 (MQ=255)
agGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTgg > 2:33356/1‑139 (MQ=255)
gCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtga > 1:420999/1‑139 (MQ=255)
cGGATGATCTTTATGCAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtgat > 2:578495/1‑139 (MQ=255)
cGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtgat < 1:77254/139‑1 (MQ=255)
ggATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtgatg < 1:500699/139‑1 (MQ=255)
tgatCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGaaa < 2:857084/139‑1 (MQ=255)
aaaCATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGaa > 2:152599/1‑139 (MQ=255)
aaCATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAAc > 2:947647/1‑139 (MQ=255)
tGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtg < 2:961683/114‑1 (MQ=255)
tGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtg > 1:961683/1‑114 (MQ=255)
gCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGt < 1:745309/110‑1 (MQ=255)
gCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGt > 2:745309/1‑110 (MQ=255)
gCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACG‑c‑cccc < 1:1029572/62‑2 (MQ=255)
gCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACG‑c‑cccc > 2:1029572/1‑61 (MQ=255)
cgcTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGgatg > 2:1100771/1‑139 (MQ=255)
gcTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGgatga < 1:1020690/139‑1 (MQ=255)
gAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAg < 1:152599/139‑1 (MQ=255)
aCCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGaa > 1:507919/1‑139 (MQ=255)
cacaGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTg > 1:1036794/1‑139 (MQ=255)
cacaGTCCCTGGCGGAGAGCGCGGCTAAACTCAACG‑CTCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATAc > 2:320130/1‑100 (MQ=255)
cacaGTCCCTGGCGGAGAGCGCGGCTAAACTCAACG‑CTCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATAc < 1:320130/100‑1 (MQ=255)
tCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtga > 2:907639/1‑87 (MQ=255)
tCCCTGGCGGAGAGCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtga < 1:907639/87‑1 (MQ=255)
agagCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTgaga > 2:406128/1‑127 (MQ=255)
agagCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTgaga < 1:406128/127‑1 (MQ=255)
agagCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTGAGACGGTGCTGTtct < 1:1100771/139‑1 (MQ=255)
agagCGCGGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTGAGACGGTGCTGTtct > 2:929411/1‑139 (MQ=255)
gcgGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTGAGACGGTGCTGTTCTCCGTg < 2:420999/139‑1 (MQ=255)
cgGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCg < 1:131334/39‑1 (MQ=255)
cgGCTAAACTCAACGCC‑CCCGGAAAGCAAACAACTGGCg > 2:131334/1‑39 (MQ=255)
aCTCAACGCC‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTGAGACGGTGCTGTTCTCCGTGCAGGAttt < 1:947647/139‑1 (MQ=255)
|
CAAGAAACTCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACG‑C‑CCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTGAGACGGTGCTGTTCTCCGTGCAGGATTT > NC_000913/2314822‑2315082
|
| 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
