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 |
|
A85 F1 I1 R1
|
15 |
51.9 |
3515760 |
95.5% |
3357550 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,558,224 |
G→A |
intergenic (‑49/+69) |
yfgK ← / ← yfgL |
GTP‑binding protein EngA/protein assembly complex, lipoprotein component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,558,224 | 0 | G | A | 96.0%
| 174.6
/ 0.2
| 50 | intergenic (‑49/+69) | yfgK/yfgL | GTP‑binding protein EngA/protein assembly complex, lipoprotein component |
| Reads supporting (aligned to +/- strand): ref base G (2/0); new base A (23/25); total (25/25) |
| Fisher's exact test for biased strand distribution p-value = 4.90e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.46e-01 |
CGACAAGCGCGACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCGCGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGAACGACAGAGACGATTAA > REL606/2558151‑2558296
|
cGACAAGCGCGACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTcacg > 2:431987/1‑76 (MQ=255)
gACAAGCGCGACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCAcgt < 1:1031733/76‑1 (MQ=255)
aCAAGCGCGACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCAcgtc > 2:659084/1‑76 (MQ=255)
aCAAGCGCGACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCAcgtc < 1:1330140/76‑1 (MQ=255)
cAAGCGCGACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCAcgtcg < 1:1026229/76‑1 (MQ=255)
aaGCGCGACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCAcgtcgt > 1:1047612/1‑76 (MQ=255)
cgcgACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCgttgt > 1:719808/1‑76 (MQ=255)
cgACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCCCGCTATATTCACGTCGTTGTTa < 2:1189716/76‑1 (MQ=255)
cgACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTa < 2:611622/76‑1 (MQ=255)
ccACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTaaaa < 1:1395517/76‑1 (MQ=255)
acaGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAAc < 1:642196/76‑1 (MQ=255)
gTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGa < 1:923033/76‑1 (MQ=255)
gTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGa < 2:1701688/76‑1 (MQ=255)
gTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGa > 2:1621933/1‑76 (MQ=255)
tACCATGTTTACAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGaaa > 2:860751/1‑76 (MQ=255)
tACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGaa < 2:352997/76‑1 (MQ=255)
tACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGaa < 2:576188/76‑1 (MQ=255)
cATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAAc < 1:19082/76‑1 (MQ=255)
aTGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACg > 1:1460100/1‑76 (MQ=255)
tttAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGcc < 1:589841/76‑1 (MQ=255)
tttAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGcc < 2:309470/76‑1 (MQ=255)
tttAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGcc < 1:652045/76‑1 (MQ=255)
ttAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGccc < 1:862808/76‑1 (MQ=255)
ctAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGcccc > 1:917662/2‑76 (MQ=255)
aaaGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCt > 2:182546/1‑76 (MQ=255)
aaaGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCt > 2:1593067/1‑76 (MQ=255)
ntCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCa > 1:704917/2‑76 (MQ=255)
tCATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAg < 2:1737782/76‑1 (MQ=255)
cATTTTTATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAgg > 1:1701277/1‑76 (MQ=255)
ttttATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGc > 1:457576/1‑76 (MQ=255)
ttATAAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCg < 2:1526304/76‑1 (MQ=255)
tataAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGt > 2:85342/1‑76 (MQ=255)
ataAATCATCAGACAACGCACGCTAAATCCACGTCGTTGTGAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGtt < 2:422117/76‑1 (MQ=255)
taAATCATCAGACAACGCACGCTATATTCGCGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGttt > 1:174964/1‑76 (MQ=255)
taAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGttt < 1:1560644/76‑1 (MQ=255)
taAATCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACACGAAAACGGCCCCTGTCCAGGAGCCGttt < 2:330280/76‑1 (MQ=255)
aaaTCATCAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGtttt < 2:384811/76‑1 (MQ=255)
atcatcAGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGGCCAGGAGCCGGTTTCa > 1:1229724/1‑76 (MQ=255)
tcatcaGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCaa < 2:788965/76‑1 (MQ=255)
catcaGCCAACGCACGCTATATTCACGTCGTTGTAAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCaaa < 2:907272/76‑1 (MQ=255)
catcaGACAACGCACGCTTGATCCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCaaa < 2:413870/76‑1 (MQ=255)
catcaGACAACGCACGCTATATTCACGTCGTTGTAAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCaaa < 1:651146/76‑1 (MQ=255)
atcaGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAg < 2:589436/76‑1 (MQ=255)
atcaGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCCGTCCCCGCGCCGGTTTCAAAg > 2:1038033/1‑76 (MQ=255)
tcaGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGt > 2:1562030/1‑76 (MQ=255)
tcaGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGt > 1:298561/1‑76 (MQ=255)
caGCCAACGCACGCTATATTCACGTCGTTGCTAAAAACAGAAAAACGGCCCCTGCCCAGGAGCCGTTTTCAAAGTg < 2:1080585/76‑1 (MQ=255)
aGACAACGCACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGa < 2:200493/76‑1 (MQ=255)
aGACAACGCACGCTATATTCAAGTCGTTGTTAAAAACAGGAAAAAGGCCCCTCTCCAGGAGCCGCTTTCAAAGTGa > 2:1228345/1‑76 (MQ=255)
aGACAACACACGCTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCCCTCCCGGGGGCGGTTTTAAAgaga > 1:1102517/1‑76 (MQ=255)
cAACGCACCTTATATTCACGTAGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGAACg < 1:1297366/76‑1 (MQ=255)
acgcacgcTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGAACGAc < 2:7517/76‑1 (MQ=255)
acgcacgcTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCCGCCCAGGAGCCGCTTTCAAAGTGAACGAc > 1:22919/1‑76 (MQ=255)
acgcacgcTATATTCACGTCGTTGTAAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCTTTTTCAAAGTGAACGAc < 2:630345/76‑1 (MQ=255)
cacgcTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGAACGACaga < 2:987463/76‑1 (MQ=255)
cacgcTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGAACGACaga > 2:172255/1‑76 (MQ=255)
acgcTATATTCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGGCGTTTTCAAAGTGAACGACagag > 2:1283430/1‑76 (MQ=255)
atTCCCGTCGTTGTTAAAAACAGGAAAACGCCCCCTGACCCGGAGCCGTTTTCAAAGTGAACGGCAGAGCCGATTa < 2:189708/76‑1 (MQ=255)
atTCACGTCGTTGTTAAAAACAGGAAAACCGCCCCTGTCCAGGAGCCCGTTTCAAAGTGAACGACAGAGAAGATTa > 1:1442248/1‑76 (MQ=255)
ttCGCGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGAACGACAGAGACGATTaa > 2:512281/1‑76 (MQ=255)
ttCACGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGAACGACAGAGACGATTaa < 2:1469784/76‑1 (MQ=255)
|
CGACAAGCGCGACCACAGGTACCATGTTTAAAGCCTCATTTTTATAAATCATCAGACAACGCACGCTATATTCGCGTCGTTGTTAAAAACAGGAAAACGGCCCCTGTCCAGGAGCCGTTTTCAAAGTGAACGACAGAGACGATTAA > REL606/2558151‑2558296
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
