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 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,657,320 |
A→G |
9.8% |
S531G (AGT→GGT) |
ppk → |
polyphosphate kinase, component of RNA degradosome |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,657,320 | 0 | A | G | 9.8%
| 140.1
/ 7.0
| 51 | S531G (AGT→GGT) | ppk | polyphosphate kinase, component of RNA degradosome |
| Reads supporting (aligned to +/- strand): ref base A (23/23); new base G (2/3); total (25/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01 |
CAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTGTATG > minE/1657251‑1657380
|
cAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAg > 1:2234805/1‑71 (MQ=255)
aaaCTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTg > 1:3596358/1‑71 (MQ=255)
aCTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg > 1:3442023/1‑70 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTa > 1:3506018/1‑71 (MQ=255)
cccGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGt > 1:2129278/1‑68 (MQ=255)
ccgccgCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTAt < 1:710066/69‑1 (MQ=255)
ccgccgCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa > 1:3454768/1‑71 (MQ=255)
ccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCAccc > 1:2395619/1‑71 (MQ=255)
ttGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg < 1:301281/56‑1 (MQ=255)
ttGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGc > 1:1097811/1‑70 (MQ=255)
gTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTTGTATCACCCTGAAGCTa < 1:602111/70‑1 (MQ=255)
gTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTa > 1:656296/1‑70 (MQ=255)
gTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTa > 1:2356101/1‑70 (MQ=255)
gTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTa < 1:1629443/70‑1 (MQ=255)
tATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa > 1:2343903/1‑58 (MQ=255)
gAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCGGTGGTATCACCCTGAAGCTAAATaa > 1:3769316/1‑71 (MQ=255)
aaaTGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCGGTg < 1:3413757/48‑1 (MQ=255)
aaaTGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCGGTGGTATCACCCTGAAGCTAAATaa < 1:1423077/70‑1 (MQ=255)
aaaTGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCAc > 1:2035896/1‑55 (MQ=255)
aaaTGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCAc > 1:3120281/1‑55 (MQ=255)
aaTGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGt < 1:689256/49‑1 (MQ=255)
aaTGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAAc < 1:3653410/70‑1 (MQ=255)
tggtggACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTaaa < 1:3580130/64‑1 (MQ=255)
ggtggACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTg > 1:1522951/1‑71 (MQ=255)
tggACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTc < 1:491835/71‑1 (MQ=255)
gACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGa > 1:3791436/1‑71 (MQ=255)
aCCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGAt < 1:1627236/71‑1 (MQ=255)
ccGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCGGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATa < 1:3677735/71‑1 (MQ=255)
ccGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATa < 1:3312993/71‑1 (MQ=255)
ccGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATa < 1:345299/71‑1 (MQ=255)
cgcgAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATa > 1:2371014/1‑70 (MQ=255)
cgAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCg > 1:2780669/1‑65 (MQ=255)
aTCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTg > 1:35183/1‑58 (MQ=255)
tCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAAc > 1:3830258/1‑53 (MQ=255)
gCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTgg < 1:3474683/70‑1 (MQ=255)
cAACGCGCAGCAAGGGCTGCGCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTg < 1:3991793/71‑1 (MQ=255)
cAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTg < 1:2803551/71‑1 (MQ=255)
cgcgCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGagc < 1:4125235/71‑3 (MQ=255)
cgcgCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATc < 1:823551/71‑1 (MQ=255)
cgcAGCAAGGGCTGCCCAGTGGTATCACGCTGAAGCTAAATAACCTTGTCGATaaa < 1:1747418/56‑1 (MQ=255)
agcaAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAATGCCTGGTTGATCGTCTg < 1:2628586/71‑1 (MQ=255)
agcaAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg < 1:601146/71‑1 (MQ=255)
agcaAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg < 1:1798984/71‑1 (MQ=255)
agcaAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg < 1:1477810/71‑1 (MQ=255)
gcaAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg < 1:3084797/70‑1 (MQ=255)
caAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTc < 1:3060099/45‑1 (MQ=255)
aaGGGCTGCCCGGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTGTAt > 1:1818536/1‑71 (MQ=255)
aaGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTGTAt > 1:3438900/1‑71 (MQ=255)
aGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAg > 1:3904707/1‑50 (MQ=255)
aGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAg > 1:1138095/1‑50 (MQ=255)
aGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTGTATg > 1:1039812/1‑71 (MQ=255)
|
CAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTGTATG > minE/1657251‑1657380
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
