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 |
2,748,276 |
A→G |
13.2% |
S117G (AGC→GGC) |
secY → |
preprotein translocase membrane subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,748,276 | 0 | A | G | 13.2%
| 176.5
/ 18.0
| 68 | S117G (AGC→GGC) | secY | preprotein translocase membrane subunit |
| Reads supporting (aligned to +/- strand): ref base A (32/27); new base G (6/3); total (38/30) |
| Fisher's exact test for biased strand distribution p-value = 7.21e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
CTGACGGTGGTTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTACCGGTCTGC > minE/2748210‑2748345
|
ctgACGGTGGTTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGc < 1:3632677/69‑1 (MQ=255)
tgACGGTGGTTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCGGc > 1:2396993/1‑68 (MQ=255)
gACGGTGGTTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAg > 1:2978706/1‑70 (MQ=255)
cGGTGGTTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAg < 1:2057322/68‑1 (MQ=255)
cGGTGGTTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTac < 1:539045/71‑1 (MQ=255)
ggtggtTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGcc < 1:2340247/65‑1 (MQ=255)
ggtggtTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTac < 1:2967821/70‑1 (MQ=255)
gtggtTAACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTacac < 1:1062179/71‑1 (MQ=255)
ttCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCGGc < 1:3164683/59‑1 (MQ=255)
ttCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAg < 1:2384452/62‑1 (MQ=255)
cACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTa > 1:1002815/1‑71 (MQ=255)
cACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTa > 1:1975001/1‑71 (MQ=255)
cccAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACg > 1:2656171/1‑71 (MQ=255)
ccAACGTTGGCATAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACgg < 1:810896/71‑1 (MQ=255)
ccAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACgg > 1:2657072/1‑71 (MQ=255)
aCGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCACTACACCCGCTACGGTAc > 1:3195060/1‑71 (MQ=255)
gTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCGGCCAGTACACCCGCTACGGTActc > 1:534881/1‑71 (MQ=255)
ttGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCGGCCa > 1:1821289/1‑50 (MQ=255)
ttGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCGGCCa > 1:2137591/1‑50 (MQ=255)
ttGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAg < 1:1633777/51‑1 (MQ=255)
ttGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTActct < 1:3297872/71‑1 (MQ=255)
ttGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTActct > 1:3315979/1‑71 (MQ=255)
ggCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTgg > 1:3945134/1‑71 (MQ=255)
gCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGc < 1:770055/45‑1 (MQ=255)
gCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGc < 1:2379727/45‑1 (MQ=255)
gAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAg < 1:1034960/45‑1 (MQ=255)
aaaTTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTg > 1:1641247/1‑71 (MQ=255)
aaTTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAg > 1:1360029/1‑43 (MQ=255)
aaTTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAg > 1:2831571/1‑43 (MQ=255)
aagaaagaAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCaa < 1:364418/70‑1 (MQ=255)
agaaagaaGGGGAGTCTGGTCGTCGTAAGATCAGc < 1:3485145/35‑1 (MQ=255)
agaagGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGc < 1:2229779/63‑1 (MQ=255)
agaagGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTc > 1:3507060/1‑70 (MQ=255)
agaagGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTc > 1:1997679/1‑70 (MQ=255)
agaagGGGAGTCTGGTCGTCGTAAGATCAGCCAGTAAACCCGCTACGGTACTCTgg > 1:2896881/1‑56 (MQ=255)
aagGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAg > 1:3582700/1‑71 (MQ=255)
aagGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAg > 1:2255660/1‑71 (MQ=255)
aagGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAg > 1:2779774/1‑71 (MQ=255)
cggggAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGc < 1:345509/59‑1 (MQ=255)
agGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAata < 1:76315/64‑1 (MQ=255)
ggggAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTc > 1:2724940/1‑71 (MQ=255)
gggAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGc < 1:163418/38‑1 (MQ=255)
gggAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCg < 1:2814779/71‑1 (MQ=255)
gggAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCg < 1:2225973/71‑1 (MQ=255)
gggAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCg < 1:1899008/71‑1 (MQ=255)
tCTGGTCGTCGTAAGATCGGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAatat < 1:186347/58‑1 (MQ=255)
tCTGGTCGTCGTAAGATCGGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAatat < 1:3059902/58‑1 (MQ=255)
tCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTg < 1:2574092/48‑1 (MQ=255)
tCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCgg < 1:834474/71‑1 (MQ=255)
tGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCa > 1:109416/1‑60 (MQ=255)
gtcgtcGTAAGATCGGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATAtt > 1:863251/1‑55 (MQ=255)
gtcgtcGTAAGATCGGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTa > 1:2238774/1‑69 (MQ=255)
gtcgtcGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCg < 1:2487941/62‑1 (MQ=255)
tcgtcgTAAGATCAGCCAGTACACCCGCTACGGTActc < 1:997474/38‑1 (MQ=255)
gtcgtAAGATCAGCCAGTACACCCGCTACGGTACTCTGGt > 1:1471062/1‑40 (MQ=255)
gtAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCaa > 1:2580474/1‑45 (MQ=255)
gtAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAata > 1:191803/1‑47 (MQ=255)
gtAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTa > 1:3271658/1‑63 (MQ=255)
gtAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTAcc > 1:1424302/1‑71 (MQ=255)
gtAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTAcc > 1:1382923/1‑71 (MQ=255)
gtAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTAcc > 1:1378169/1‑71 (MQ=255)
gtAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTAcc > 1:2864117/1‑71 (MQ=255)
tAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTACCg < 1:2456347/71‑1 (MQ=255)
aaGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTACCgg > 1:3575348/1‑71 (MQ=255)
aGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTACCGGt > 1:1809753/1‑71 (MQ=255)
tCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCt > 1:3045089/1‑62 (MQ=255)
tCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTACCGGTCTg > 1:371118/1‑71 (MQ=255)
cAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTACCGGTCTGc > 1:378427/1‑71 (MQ=255)
|
CTGACGGTGGTTCACCCAACGTTGGCAGAAATTAAGAAAGAAGGGGAGTCTGGTCGTCGTAAGATCAGCCAGTACACCCGCTACGGTACTCTGGTGCTGGCAATATTCCAGTCGATCGGTATTGCTACCGGTCTGC > minE/2748210‑2748345
|
| 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
