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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,788,749 |
C→T |
23.1% |
P38S (CCG→TCG) |
ygaF → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,788,749 | 0 | C | T | 23.1%
| 74.5
/ 19.4
| 39 | P38S (CCG→TCG) | ygaF | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (15/15); new base T (6/3); total (21/18) |
| Fisher's exact test for biased strand distribution p-value = 4.64e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01 |
TCGACCGCCATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCT > W3110S.gb/2788680‑2788819
|
tCGACCGCCATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTTGAAAAAGAGTCCGcccc > 1:1491669/1‑71 (MQ=255)
cGACCGCCATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCg > 1:3943773/1‑71 (MQ=255)
ccATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGcccc > 1:4172244/1‑64 (MQ=255)
ccATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGt > 1:4090732/1‑71 (MQ=255)
ccATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGt > 1:1801427/1‑71 (MQ=255)
cATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTc < 1:3561878/71‑1 (MQ=255)
cAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGcc > 1:2948275/1‑63 (MQ=255)
cAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGCCTGTCAc > 1:127075/1‑69 (MQ=255)
cAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCa > 1:2421576/1‑68 (MQ=255)
cAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCa < 1:3874954/71‑1 (MQ=255)
aCTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCt < 1:1037221/62‑1 (MQ=255)
aCTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCt < 1:2713503/62‑1 (MQ=255)
cTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGAc > 1:4494040/1‑71 (MQ=255)
cTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGAc > 1:3134917/1‑71 (MQ=255)
gattgatGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGcc > 1:1047995/1‑58 (MQ=255)
gattgatGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACgg > 1:1244053/1‑71 (MQ=255)
atGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCcac < 1:146652/71‑1 (MQ=255)
tGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCcac > 1:2652899/1‑70 (MQ=255)
tCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCt > 1:4088520/1‑51 (MQ=255)
tCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCacaac < 1:853138/71‑1 (MQ=255)
tCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCacaac < 1:1815451/71‑1 (MQ=255)
gCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGAt > 1:3693672/1‑71 (MQ=255)
cATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGCCTGTCACCAGACGGGCCACAACAg < 1:119976/57‑1 (MQ=255)
cATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGCCTGTCACCAGACGGGCCACAACAg < 1:2861830/57‑1 (MQ=255)
cATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCt < 1:1202321/35‑1 (MQ=255)
ttGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGa < 1:3098969/42‑1 (MQ=255)
ttGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATc < 1:2123850/65‑1 (MQ=255)
ttGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGcc < 1:2889440/71‑1 (MQ=255)
ttGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGcc > 1:4149148/1‑71 (MQ=255)
gCGTTGCTGGAAAAAGAGTCCGCCTCGGCCTGTCACCAGACGGGCcac > 1:445474/1‑48 (MQ=255)
gCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCa > 1:4571879/1‑35 (MQ=255)
gCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCgg > 1:3293561/1‑71 (MQ=255)
ttGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCggg < 1:2756498/69‑1 (MQ=255)
cTGGAAAAAGAGTCCGCCTCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCt < 1:2405928/70‑1 (MQ=255)
cTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCt < 1:3344603/70‑1 (MQ=255)
gAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTAt < 1:4187847/69‑1 (MQ=255)
aaaaaGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGAt > 1:651596/1‑52 (MQ=255)
aaaaaGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCgggg > 1:3972478/1‑63 (MQ=255)
gagTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGcc > 1:324871/1‑71 (MQ=255)
cGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCa < 1:3525094/71‑1 (MQ=255)
gCCTCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAg > 1:1989703/1‑71 (MQ=255)
ccGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCt < 1:2910574/71‑1 (MQ=255)
ccGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCt < 1:2097225/71‑1 (MQ=255)
|
TCGACCGCCATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCT > W3110S.gb/2788680‑2788819
|
| 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
