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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,547,976 |
T→C |
24.6% |
V62A (GTT→GCT) |
htrL → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,547,976 | 0 | T | C | 24.6%
| 114.4
/ 40.4
| 69 | V62A (GTT→GCT) | htrL | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (29/23); new base C (6/11); total (35/34) |
| Fisher's exact test for biased strand distribution p-value = 1.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.88e-01 |
ACTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGATATATC > minE/2547907‑2548046
|
aCTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGt < 1:1326383/70‑1 (MQ=255)
cTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGtt < 1:2640431/70‑1 (MQ=255)
cTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGtt < 1:2846730/70‑1 (MQ=255)
cTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTg < 1:2807373/71‑1 (MQ=255)
cTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTg < 1:454972/71‑1 (MQ=255)
tttGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTg > 1:2289769/1‑70 (MQ=255)
tGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTg < 1:294537/68‑1 (MQ=255)
tGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAg > 1:1117403/1‑71 (MQ=255)
tGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGa < 1:139424/69‑1 (MQ=255)
cGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGAt < 1:3876381/71‑1 (MQ=255)
cGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGAt < 1:809705/71‑1 (MQ=255)
gTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGa < 1:1466962/64‑1 (MQ=255)
gTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGa < 1:3807866/64‑1 (MQ=255)
tCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTc > 1:1694977/1‑71 (MQ=255)
cTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAg > 1:3326733/1‑64 (MQ=255)
tGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGa > 1:2887786/1‑66 (MQ=255)
gCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCaa > 1:3347494/1‑71 (MQ=255)
aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa < 1:1828544/71‑1 (MQ=255)
aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGa > 1:3886053/1‑70 (MQ=255)
cTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCg > 1:3799387/1‑57 (MQ=255)
cTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGa > 1:3740408/1‑58 (MQ=255)
cTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACgg < 1:3279026/68‑1 (MQ=255)
cTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa < 1:3401834/70‑1 (MQ=255)
gAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGAt > 1:2083114/1‑56 (MQ=255)
aaaaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAAcc < 1:1326830/70‑1 (MQ=255)
aaaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaa > 1:1504287/1‑71 (MQ=255)
aaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaa > 1:1523512/1‑70 (MQ=255)
aTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaaca < 1:621564/71‑1 (MQ=255)
tGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaacaa < 1:2657499/71‑1 (MQ=255)
tGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCaa > 1:1072089/1‑57 (MQ=255)
tGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaacaa < 1:1396979/71‑1 (MQ=255)
agaTGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGTAGCGATTCGCAACGGAAAACCaacaac < 1:87451/70‑1 (MQ=255)
tgatTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGa < 1:3920291/40‑1 (MQ=255)
tgatTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGa < 1:3924701/40‑1 (MQ=255)
attattTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCaa > 1:2784488/1‑50 (MQ=255)
attattTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAAc > 1:3850083/1‑51 (MQ=255)
attattTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAAc > 1:3204233/1‑51 (MQ=255)
attTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGAtt > 1:1855687/1‑42 (MQ=255)
tttCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgtta > 1:1864818/1‑71 (MQ=255)
ttCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgtta < 1:1546665/70‑1 (MQ=255)
cACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttatc > 1:3476885/1‑70 (MQ=255)
aCTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGttatcgttatcg < 1:3168280/70‑1 (MQ=255)
ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat < 1:3181552/61‑1 (MQ=255)
ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat < 1:2984744/61‑1 (MQ=255)
ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat < 1:495000/61‑1 (MQ=255)
ccGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaaa < 1:1812268/71‑1 (MQ=255)
cGATTTGAAACCAAGTGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaaaa < 1:1022145/71‑1 (MQ=255)
gATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGat > 1:3021144/1‑63 (MQ=255)
aTTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaaa > 1:408230/1‑68 (MQ=255)
aTTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaaa > 1:1158664/1‑68 (MQ=255)
aTTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaaa > 1:1126847/1‑68 (MQ=255)
tttGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAg > 1:2391667/1‑70 (MQ=255)
tttGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAg > 1:2554307/1‑70 (MQ=255)
tttGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGa < 1:2904482/71‑1 (MQ=255)
ttGAAACCAAGGGTTGAAGCGATTCGCAACGGaaa > 1:1197627/1‑35 (MQ=255)
ttGAAACCAAGGGTTGAAGCGATTCGCAACGGaaa > 1:168144/1‑35 (MQ=255)
tGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaa > 1:2167975/1‑39 (MQ=255)
gAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaaa < 1:1788448/64‑1 (MQ=255)
aCCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGata > 1:3716/1‑56 (MQ=255)
ccAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAAtt > 1:683319/1‑68 (MQ=255)
ccAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAg < 1:699777/71‑1 (MQ=255)
cAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGatat > 1:3224637/1‑55 (MQ=255)
cAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgt < 1:3549699/46‑1 (MQ=255)
cAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgt < 1:3049943/46‑1 (MQ=255)
cAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGa < 1:976444/71‑1 (MQ=255)
aGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGata > 1:2302610/1‑52 (MQ=255)
aGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGata < 1:2327579/71‑1 (MQ=255)
gggTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcg > 1:2217382/1‑42 (MQ=255)
gggTTGAAGCGATTCGCAACGGAAAACCAACAACGGGTATCGTTATCGATATAAAAAAGAAATTTAGatat < 1:3126475/71‑1 (MQ=255)
ggTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgtt > 1:2150753/1‑43 (MQ=255)
ggTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGatata < 1:914000/71‑1 (MQ=255)
gTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGatatat > 1:3271999/1‑71 (MQ=255)
ttGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGATATATc < 1:1095208/71‑1 (MQ=255)
|
ACTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGATATATC > minE/2547907‑2548046
|
| 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
