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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,593,753 |
C→T |
40.3% |
G40G (GGG→GGA) |
cysA ← |
sulfate/thiosulfate transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,593,753 | 0 | C | T | 40.3%
| 19.5
/ 29.6
| 47 | G40G (GGG→GGA) | cysA | sulfate/thiosulfate transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (15/13); new base T (14/5); total (29/18) |
| Fisher's exact test for biased strand distribution p-value = 2.26e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.86e-01 |
GCGAATATGCCCGCTGGTTTGATGCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAATATCCAGTGAGATATCGTT > minE/1593693‑1593818
|
gCGAATATGCCCGCTGGTTTGATGCTCCAGCCCGG‑GGTAATGCGCAGCAGCGTGGTTTTCCCGGAACCg < 1:2360902/69‑1 (MQ=255)
cGAATATGCCCGCTGGTTTGATGCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCg < 1:3121051/69‑1 (MQ=255)
atGCCCGCTGGTTTGATGCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACgg > 1:3091740/1‑69 (MQ=255)
atGCCCGCTGGTTTGATGCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACgg > 1:1619603/1‑69 (MQ=255)
cccGCTGGTTTGATGCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGc > 1:2873079/1‑67 (MQ=255)
cTGGTTTGATGCTCCAGCCCGGCAATAATGCGCAGCAGCGTGGTTTTTCCGGAACCGGACGGCCCCAGc < 1:924089/69‑1 (MQ=37)
cTGGTTTGATGCTCCAGCCCGGCAATAATGCGCAGCAGCGTGGTTTTTCCGGAACCGGACGGCCCCAGc < 1:3105753/69‑1 (MQ=37)
cTGGTTTGATGCTCCAGCCCGGCAATAATGCGCAGCAGCGTGGTTTTTCCGGAACCGGACGGCCCCAGc < 1:3035152/69‑1 (MQ=37)
cTGGTTTGATGCTCCAGCCCGGCAATAATGCGCAGCAGCGTGGTTTTTCCGGAACCGGACGGCCCCAGc < 1:262077/69‑1 (MQ=37)
gCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGAcc < 1:1315402/68‑1 (MQ=255)
gCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGAcc < 1:953453/68‑1 (MQ=255)
gCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCa < 1:834347/69‑1 (MQ=255)
gCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCa < 1:2002717/69‑1 (MQ=255)
gCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCa < 1:1330207/69‑1 (MQ=255)
caaTAATGCGCAGCAGCGTGGTTTTTCCGGAACCGGACGGCCCCAGc < 1:2274794/45‑1 (MQ=37)
gATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAgg < 1:2602195/69‑1 (MQ=255)
gATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAgg < 1:873390/69‑1 (MQ=255)
gATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAgg > 1:2651794/1‑69 (MQ=255)
gATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAgg > 1:3337009/1‑69 (MQ=255)
gATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAgg > 1:3152942/1‑69 (MQ=255)
aaTGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCaa > 1:390108/1‑45 (MQ=255)
aaTGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAat > 1:795493/1‑69 (MQ=255)
aaTGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAat > 1:2835837/1‑69 (MQ=255)
aaTGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAat > 1:670161/1‑69 (MQ=255)
aaTGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAat > 1:3194559/1‑69 (MQ=255)
aTGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAata < 1:2410807/69‑1 (MQ=255)
aTGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAata > 1:1408995/1‑69 (MQ=255)
cgcAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAATATcc > 1:2468145/1‑69 (MQ=255)
cgcAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAATATcc > 1:1505902/1‑69 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATcct > 1:1057796/1‑67 (MQ=39)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:1806540/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:2370663/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:2552338/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:2628641/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:857901/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:2786179/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:727354/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:1343818/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:3022394/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:340128/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:3384221/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATATCCa > 1:1682218/1‑68 (MQ=255)
cagcagCGTGGTTTTTCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCAGAAGGAATAACCa > 1:2735403/1‑68 (MQ=39)
cagcGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAATATCCa > 1:3397017/1‑65 (MQ=255)
tttCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGTAATATCCAGTGAGATATCGtt < 1:3219606/69‑1 (MQ=255)
tttCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAATATCCAGTGAGATATCGtt < 1:894592/69‑1 (MQ=255)
tttCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAATATCCAGTGAGATATCGtt < 1:3205831/69‑1 (MQ=255)
cccGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAATATCCAGTGAGATATCGtt < 1:482589/66‑1 (MQ=255)
|
GCGAATATGCCCGCTGGTTTGATGCTCCAGCCCGGCGATAATGCGCAGCAGCGTGGTTTTCCCGGAACCGGACGGCCCCAGCAACGCGACCATCTGACCTGAAGGAATATCCAGTGAGATATCGTT > minE/1593693‑1593818
|
| 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
