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 |
|
A1 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,611,108 |
T→C |
8.3% |
F185L (TTC→CTC) |
hyfR → |
DNA‑binding transcriptional activator, formate sensing |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,611,108 | 0 | T | C | 8.3%
| 190.8
/ 9.3
| 72 | F185L (TTC→CTC) | hyfR | DNA‑binding transcriptional activator, formate sensing |
| Reads supporting (aligned to +/- strand): ref base T (30/36); new base C (4/2); total (34/38) |
| Fisher's exact test for biased strand distribution p-value = 4.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01 |
CAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTGTGGTGC > W3110S.gb/2611043‑2611176
|
cAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCgg > 1:1646862/1‑70 (MQ=255)
cAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTCACGTCGCTCGTGAGATCCATCATTTTTTCgg < 1:2495139/70‑1 (MQ=255)
gTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCt > 1:839802/1‑71 (MQ=255)
tGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCg < 1:1814060/66‑1 (MQ=255)
tGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCg < 1:2164898/66‑1 (MQ=255)
tGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTg > 1:2094545/1‑71 (MQ=255)
gCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTg < 1:1671756/70‑1 (MQ=255)
cTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGc > 1:2394375/1‑71 (MQ=255)
tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCg < 1:2804746/61‑1 (MQ=255)
tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCg < 1:2208569/61‑1 (MQ=255)
tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCg < 1:75659/61‑1 (MQ=255)
tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCt < 1:543874/69‑1 (MQ=255)
tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCt < 1:1603869/69‑1 (MQ=255)
acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCgg < 1:2272394/60‑1 (MQ=255)
acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc > 1:701466/1‑62 (MQ=255)
acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc > 1:2318933/1‑62 (MQ=255)
acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag > 1:1424102/1‑71 (MQ=255)
caTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagt < 1:2047912/71‑1 (MQ=255)
aTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtc < 1:305431/71‑1 (MQ=255)
tCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagt > 1:1311602/1‑69 (MQ=255)
tCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagt > 1:1759160/1‑69 (MQ=255)
cTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc > 1:1109522/1‑58 (MQ=255)
ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc > 1:2775985/1‑57 (MQ=255)
ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc > 1:1822769/1‑57 (MQ=255)
ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag > 1:1939169/1‑70 (MQ=255)
ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag > 1:1353851/1‑70 (MQ=255)
ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag > 1:1311705/1‑70 (MQ=255)
ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTtcagtcag > 1:2799543/1‑70 (MQ=255)
gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag < 1:2402746/68‑1 (MQ=255)
gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag < 1:1634909/68‑1 (MQ=255)
aTCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag < 1:1767023/67‑1 (MQ=255)
aTCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag < 1:280328/67‑1 (MQ=255)
aTCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTAt < 1:1595709/70‑1 (MQ=255)
aTCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTAt < 1:2014153/70‑1 (MQ=255)
aTCTCGACGATCTCATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag < 1:2187305/67‑1 (MQ=255)
tctcGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt < 1:1050297/59‑1 (MQ=255)
tctcGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTa > 1:2741355/1‑68 (MQ=255)
gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATgg < 1:1667081/67‑1 (MQ=255)
gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATgg < 1:637723/67‑1 (MQ=255)
gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGt < 1:95976/68‑1 (MQ=255)
gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGt < 1:1526901/68‑1 (MQ=255)
gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTa > 1:1191023/1‑69 (MQ=255)
gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTATg < 1:1501729/66‑1 (MQ=255)
gacgaTCTGATCGCTGACGTAGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATg < 1:1270098/66‑1 (MQ=255)
gacgaTCTGATCGCTGAAGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTa > 1:2197939/1‑69 (MQ=255)
acgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCt < 1:1930365/49‑1 (MQ=255)
acgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCt < 1:46518/49‑1 (MQ=255)
acgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCt < 1:2401533/49‑1 (MQ=255)
acgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCt < 1:2587194/49‑1 (MQ=255)
gaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTa > 1:2251268/1‑61 (MQ=255)
cTGATCGCTGACGTCGCTCGTGAGATCCATCAttttt > 1:2341036/1‑37 (MQ=255)
cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag > 1:1320597/1‑56 (MQ=255)
cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTggg > 1:1711046/1‑68 (MQ=255)
cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGa > 1:569394/1‑71 (MQ=255)
cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGa > 1:769892/1‑71 (MQ=255)
aTCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGatc < 1:2357824/70‑1 (MQ=255)
aCGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAg < 1:1947936/71‑1 (MQ=255)
gTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtca > 1:864988/1‑39 (MQ=255)
gCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTa > 1:521032/1‑48 (MQ=255)
cTCGTGAGATCCATCATTTTTTCGGTCTGGCTTTAGTCAGTATGGTACTGGGCGATCATCGAAAGAACgag < 1:1320548/71‑1 (MQ=255)
cTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACgag < 1:777825/71‑1 (MQ=255)
cTCGTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACgag < 1:589604/71‑1 (MQ=255)
tGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGt < 1:1795966/42‑1 (MQ=255)
tGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGt < 1:1770873/71‑1 (MQ=255)
agaTCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGaaa > 1:2433391/1‑58 (MQ=255)
agaTCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGtt > 1:2757198/1‑70 (MQ=255)
agaTCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGtt > 1:496327/1‑70 (MQ=255)
ccATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGcc > 1:1981257/1‑71 (MQ=255)
tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtgt > 1:1826388/1‑71 (MQ=255)
tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtgt < 1:2000676/71‑1 (MQ=255)
atTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGaa > 1:2231152/1‑52 (MQ=255)
atTTTTTCGGTCTGGCTTCAGTAAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtgg > 1:1490114/1‑71 (MQ=255)
atTTTCTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGatca > 1:2434365/1‑43 (MQ=255)
tttCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTGTGGTGc < 1:2061900/70‑1 (MQ=255)
|
CAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTGTGGTGC > W3110S.gb/2611043‑2611176
|
| 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
