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 |
2,729,684 |
T→C |
32.5% |
noncoding (130/1542 nt) |
rrsG ← |
16S ribosomal RNA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,729,684 | 0 | T | C | 32.5%
| 44.7
/ 33.8
| 40 | noncoding (130/1542 nt) | rrsG | 16S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base T (18/9); new base C (5/8); total (23/17) |
| Fisher's exact test for biased strand distribution p-value = 1.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.05e-01 |
CTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGTTACCGTTCGAC > W3110S.gb/2729614‑2729753
|
ctctTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCt > 1:2406617/1‑71 (MQ=38)
ctctTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCt > 1:1731388/1‑71 (MQ=38)
tttGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTcc > 1:3181789/1‑71 (MQ=39)
tttGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTcc > 1:3296132/1‑71 (MQ=39)
ttGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTcc > 1:757569/1‑70 (MQ=40)
gTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCCTCCCa < 1:3533410/69‑1 (MQ=255)
cTTGCGACATTATGAGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACa > 1:1376172/1‑71 (MQ=255)
tGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACAt > 1:2246404/1‑70 (MQ=40)
gCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACAt < 1:1047445/69‑1 (MQ=40)
gCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCCTCCCAGACAtt < 1:3022790/70‑1 (MQ=255)
gACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACt < 1:2149117/71‑1 (MQ=39)
gACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCCTCCCAGACATTACt > 1:2389305/1‑71 (MQ=255)
ttATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACTc < 1:2796347/68‑1 (MQ=35)
aTGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCCTCCCAGACATTACTCACCCg > 1:3016093/1‑71 (MQ=21)
gTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGa < 1:4333395/53‑1 (MQ=35)
ttAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGa < 1:4625322/50‑1 (MQ=38)
ttAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCCTCCCAGACATTACTCACCCGTCCGCCa < 1:3923559/70‑1 (MQ=25)
tACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGt > 1:465173/1‑70 (MQ=35)
tCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAag > 1:885734/1‑71 (MQ=35)
tagtTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAgcagca < 1:4445537/71‑1 (MQ=39)
tagtTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAgcagca < 1:4061582/71‑1 (MQ=39)
gtTATCCCCCTCCATCAGTCAGCCTCCCAGACATTAc < 1:106945/37‑1 (MQ=14)
gtTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAg > 1:1772905/1‑71 (MQ=39)
ttATCCCCCTCCATCAGGCAGCCTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAgc < 1:1653190/71‑1 (MQ=255)
aTCCCCCTCCATCAGGCAGGCTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAgct < 1:1609869/70‑1 (MQ=255)
aTCCCCCTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAgct > 1:3494825/1‑70 (MQ=40)
cccccTCCATCAGGCAGCCTCCCAGACATTACTCAcc > 1:1916750/1‑37 (MQ=255)
cccccTCCATCAGGCAGCCTCCCAGACATTACTCACCCGTCCGCCACTCGTCAg > 1:1911320/1‑54 (MQ=255)
cccccTCCATCAGGCAGCCTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAgctgct > 1:1167596/1‑71 (MQ=255)
cTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACt > 1:2219382/1‑44 (MQ=38)
cTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCt < 1:3309452/71‑1 (MQ=255)
tCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGt > 1:4391175/1‑46 (MQ=38)
tCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAgcagca > 1:2152946/1‑59 (MQ=255)
aTCAGGCAGCTTCCCAGACATTACTCACCCGTCCg > 1:3082053/1‑35 (MQ=40)
tCATGCAGCCTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGt < 1:4207818/68‑1 (MQ=255)
tCATGCAGCCTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGt < 1:4212974/68‑1 (MQ=255)
tCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCGACTCGTCAGCGAAGCAGCAAg > 1:2920237/1‑57 (MQ=255)
tCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGt > 1:1649721/1‑68 (MQ=255)
aGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGTTACCg > 1:3343567/1‑71 (MQ=255)
ggCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAg > 1:2926429/1‑54 (MQ=255)
aGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTg > 1:3315868/1‑61 (MQ=255)
cTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGTTACCGTTCGAc < 1:751431/71‑1 (MQ=40)
|
CTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGCTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGTTACCGTTCGAC > W3110S.gb/2729614‑2729753
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
