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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,706,728 |
G→A |
48.9% |
P228L (CCA→CTA) |
rseB ← |
anti‑sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,706,728 | 0 | G | A | 48.9%
| ‑0.7
/ 64.5
| 45 | P228L (CCA→CTA) | rseB | anti‑sigma factor |
| Reads supporting (aligned to +/- strand): ref base G (4/19); new base A (13/9); total (17/28) |
| Fisher's exact test for biased strand distribution p-value = 5.80e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.82e-01 |
CGATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGC > W3110S.gb/2706663‑2706784
|
cGATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCa < 1:1202865/69‑1 (MQ=255)
aGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCa > 1:70243/1‑69 (MQ=255)
ggCATTTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg < 1:3636747/69‑1 (MQ=255)
ggCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg < 1:2620119/69‑1 (MQ=255)
cATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAgg < 1:2255490/68‑1 (MQ=255)
aTGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGtt < 1:2019673/69‑1 (MQ=255)
ttgtCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGc > 1:1204805/1‑69 (MQ=255)
ttgtCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGc < 1:165481/69‑1 (MQ=255)
ttgtCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGc < 1:1658133/69‑1 (MQ=255)
ccATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTc < 1:965658/68‑1 (MQ=255)
ccATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTc < 1:1897455/68‑1 (MQ=255)
ccATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTc < 1:1718532/68‑1 (MQ=255)
ccATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTc < 1:1488745/68‑1 (MQ=255)
cATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTc < 1:3005080/67‑1 (MQ=255)
aTCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg > 1:1792485/1‑57 (MQ=255)
aTCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg > 1:1225948/1‑57 (MQ=255)
tcgtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAg > 1:423040/1‑68 (MQ=255)
gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAg < 1:517310/54‑1 (MQ=255)
gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAg < 1:2222726/54‑1 (MQ=255)
gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGc > 1:1069930/1‑48 (MQ=255)
gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGc > 1:2778129/1‑48 (MQ=255)
gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGc > 1:1340359/1‑48 (MQ=255)
gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTg > 1:3348126/1‑69 (MQ=255)
cgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGaa < 1:530927/69‑1 (MQ=255)
cGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAAcc > 1:2671420/1‑40 (MQ=255)
gACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCt < 1:2326454/62‑1 (MQ=255)
actactGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCt < 1:2099933/61‑1 (MQ=255)
actGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTAc < 1:2684945/69‑1 (MQ=255)
actGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTAc < 1:416148/69‑1 (MQ=255)
gAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAgg > 1:2978298/1‑68 (MQ=255)
gAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAgg > 1:2141995/1‑68 (MQ=255)
gAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAgg > 1:145793/1‑68 (MQ=255)
aaCTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAAtt < 1:3722766/47‑1 (MQ=255)
aCTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACa < 1:540544/69‑1 (MQ=255)
ttCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCt > 1:1609064/1‑58 (MQ=255)
ttCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACa > 1:1255799/1‑67 (MQ=255)
ttCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGa < 1:1427705/69‑1 (MQ=255)
gCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGaaa > 1:3612667/1‑68 (MQ=255)
gCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGaaa > 1:3176357/1‑68 (MQ=255)
tAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGc < 1:2202884/68‑1 (MQ=255)
tAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGc < 1:227146/68‑1 (MQ=255)
tAAAACCCTGTGGAAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGc < 1:1871351/68‑1 (MQ=255)
tAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGc < 1:830924/68‑1 (MQ=255)
aCCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCt < 1:699727/40‑1 (MQ=255)
aCCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCt < 1:765569/40‑1 (MQ=255)
|
CGATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGC > W3110S.gb/2706663‑2706784
|
| 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
