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 |
1,463,502 |
C→T |
73.9% |
P299L (CCG→CTG) |
paaJ → |
predicted beta‑ketoadipyl CoA thiolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,463,502 | 0 | C | T | 73.9%
| 33.4
/ 12.4
| 23 | P299L (CCG→CTG) | paaJ | predicted beta‑ketoadipyl CoA thiolase |
| Reads supporting (aligned to +/- strand): ref base C (2/4); new base T (11/6); total (13/10) |
| Fisher's exact test for biased strand distribution p-value = 3.41e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01 |
GCGGGCGCGTATCGTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGT > W3110S.gb/1463440‑1463562
|
gcgGGCGCGTATCGTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGcc > 1:175755/1‑69 (MQ=255)
tCGTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGcc > 1:2752277/1‑69 (MQ=255)
tCGTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGcc > 1:973490/1‑69 (MQ=255)
gTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCgg > 1:1326910/1‑69 (MQ=255)
gCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGaa > 1:3149417/1‑69 (MQ=255)
gCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGaa > 1:259654/1‑69 (MQ=255)
gCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGa < 1:1353966/68‑1 (MQ=255)
aaCCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAAcg > 1:3021995/1‑69 (MQ=255)
ggAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAg < 1:425270/69‑1 (MQ=255)
ggAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAg < 1:492727/69‑1 (MQ=255)
cgcgCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAg > 1:2077749/1‑64 (MQ=255)
gcgcCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTc > 1:2494015/1‑68 (MQ=255)
gcgcCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTc > 1:3402357/1‑68 (MQ=255)
gcgcCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTc > 1:716813/1‑68 (MQ=255)
gcgcCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCCCAGGGCTGAGTATTc > 1:2681022/1‑68 (MQ=255)
ccTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGa < 1:1726702/69‑1 (MQ=255)
ccTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGAGCAGGGCTGAGTATTCACGa < 1:3037848/69‑1 (MQ=255)
gggCTTGGTCTGGTGCCTGCAATTCGCCGGGTGCTgg < 1:3468466/37‑1 (MQ=37)
gggCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTgg < 1:1431904/37‑1 (MQ=255)
gCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGt < 1:2310522/69‑1 (MQ=255)
gCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGt < 1:1613192/69‑1 (MQ=255)
gCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGt < 1:805868/69‑1 (MQ=255)
tGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGat > 1:2870424/1‑58 (MQ=255)
|
GCGGGCGCGTATCGTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGT > W3110S.gb/1463440‑1463562
|
| 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
