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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,719,476 |
C→T |
46.6% |
intergenic (+65/+2) |
argD → / ← yhfK |
bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase/conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,719,476 | 0 | C | T | 46.6%
| 5.4
/ 49.1
| 60 | intergenic (+65/+2) | argD/yhfK | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase/conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (18/14); new base T (14/14); total (32/28) |
| Fisher's exact test for biased strand distribution p-value = 7.96e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01 |
AAATACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACGC > minE/2719410‑2719538
|
aaaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAt < 1:2124021/69‑1 (MQ=255)
aaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAtt > 1:995093/1‑69 (MQ=255)
aaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAtt > 1:956857/1‑69 (MQ=255)
aaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAtt > 1:436325/1‑69 (MQ=255)
aaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAtt > 1:14943/1‑69 (MQ=255)
aaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAtt > 1:1895044/1‑69 (MQ=255)
aaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAtt > 1:592141/1‑69 (MQ=255)
aaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAt > 1:1891139/1‑68 (MQ=255)
aaTACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAt > 1:1507715/1‑68 (MQ=255)
cGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAt > 1:1346155/1‑64 (MQ=255)
cGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAt > 1:391069/1‑64 (MQ=255)
cGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAt > 1:1597324/1‑64 (MQ=255)
cGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCAt > 1:543089/1‑64 (MQ=255)
cAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAAt > 1:2280658/1‑69 (MQ=255)
cAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAAt > 1:503592/1‑69 (MQ=255)
cAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAAt > 1:1660576/1‑69 (MQ=255)
aGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAAc > 1:2226074/1‑69 (MQ=255)
gcgTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCa < 1:465613/69‑1 (MQ=255)
gcgTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCa < 1:1703227/69‑1 (MQ=255)
gcgTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCa < 1:1428306/69‑1 (MQ=255)
gcgTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCa < 1:2505016/69‑1 (MQ=255)
gcgTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCa < 1:3340632/69‑1 (MQ=255)
aTGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:927141/1‑69 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAAc > 1:1996212/3‑48 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:2503911/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:2840314/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:2496438/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:3125490/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:319886/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:335810/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:2423788/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:722012/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:1061660/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:2371609/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:1599128/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:1779357/3‑68 (MQ=255)
caccTCATCCGATGGTTTAGCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATccc > 1:2025678/3‑68 (MQ=255)
ccTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTg > 1:754499/1‑69 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:418150/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:1237154/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:861120/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:1683064/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:1700462/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:1979245/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:2439489/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:3357937/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:2199613/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:3114204/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:2334010/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:1057280/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGCCgc < 1:2425424/68‑1 (MQ=255)
gCCTGTATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTCATGCGGTCGCTGCCgc < 1:1651793/68‑1 (MQ=255)
gCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACgc < 1:200704/68‑1 (MQ=255)
gCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACgc < 1:2091785/68‑1 (MQ=255)
gCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACgc < 1:1774583/68‑1 (MQ=255)
gCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACgc < 1:2246526/68‑1 (MQ=255)
gCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACgc < 1:639609/68‑1 (MQ=255)
gCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACgc < 1:745838/68‑1 (MQ=255)
gCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACgc < 1:2782407/68‑1 (MQ=255)
gCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGGCGCTGACgc < 1:2561054/68‑1 (MQ=255)
|
AAATACGAAGCATCAGGCAAAAGATGTCGGATGCGGCGTGAATGCCTTATCCGATGGTTTAGCCTGCATTACGCCTTCGAATCCCGCAACTTGCGACTCAGCCAAATCCCGTGATGCGGTCGCTGACGC > minE/2719410‑2719538
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
